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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs7580472

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:241083611 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.170773 (45202/264690, TOPMED)
G=0.166786 (23357/140042, GnomAD)
G=0.24253 (6853/28256, 14KJPN) (+ 16 more)
G=0.13261 (2505/18890, ALFA)
G=0.24457 (4099/16760, 8.3KJPN)
G=0.1989 (1274/6404, 1000G_30x)
G=0.1925 (964/5008, 1000G)
G=0.0795 (356/4480, Estonian)
G=0.0906 (349/3854, ALSPAC)
G=0.0928 (344/3708, TWINSUK)
G=0.2406 (705/2930, KOREAN)
G=0.081 (81/998, GoNL)
G=0.103 (62/600, NorthernSweden)
G=0.218 (47/216, Qatari)
G=0.160 (34/212, Vietnamese)
A=0.416 (74/178, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
A=0.50 (9/18, Siberian)
G=0.50 (9/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTERF4 : Intron Variant
SNED1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 A=0.86739 G=0.13261
European Sub 14286 A=0.90907 G=0.09093
African Sub 2946 A=0.6701 G=0.3299
African Others Sub 114 A=0.596 G=0.404
African American Sub 2832 A=0.6730 G=0.3270
Asian Sub 112 A=0.848 G=0.152
East Asian Sub 86 A=0.80 G=0.20
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.801 G=0.199
Latin American 2 Sub 610 A=0.905 G=0.095
South Asian Sub 98 A=0.91 G=0.09
Other Sub 692 A=0.825 G=0.175


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 A=0.829227 G=0.170773
gnomAD - Genomes Global Study-wide 140042 A=0.833214 G=0.166786
gnomAD - Genomes European Sub 75878 A=0.90750 G=0.09250
gnomAD - Genomes African Sub 41922 A=0.67308 G=0.32692
gnomAD - Genomes American Sub 13646 A=0.90701 G=0.09299
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8637 G=0.1363
gnomAD - Genomes East Asian Sub 3118 A=0.8021 G=0.1979
gnomAD - Genomes Other Sub 2154 A=0.8635 G=0.1365
14KJPN JAPANESE Study-wide 28256 A=0.75747 G=0.24253
Allele Frequency Aggregator Total Global 18890 A=0.86739 G=0.13261
Allele Frequency Aggregator European Sub 14286 A=0.90907 G=0.09093
Allele Frequency Aggregator African Sub 2946 A=0.6701 G=0.3299
Allele Frequency Aggregator Other Sub 692 A=0.825 G=0.175
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.905 G=0.095
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.801 G=0.199
Allele Frequency Aggregator Asian Sub 112 A=0.848 G=0.152
Allele Frequency Aggregator South Asian Sub 98 A=0.91 G=0.09
8.3KJPN JAPANESE Study-wide 16760 A=0.75543 G=0.24457
1000Genomes_30x Global Study-wide 6404 A=0.8011 G=0.1989
1000Genomes_30x African Sub 1786 A=0.6081 G=0.3919
1000Genomes_30x Europe Sub 1266 A=0.8910 G=0.1090
1000Genomes_30x South Asian Sub 1202 A=0.9218 G=0.0782
1000Genomes_30x East Asian Sub 1170 A=0.7940 G=0.2060
1000Genomes_30x American Sub 980 A=0.897 G=0.103
1000Genomes Global Study-wide 5008 A=0.8075 G=0.1925
1000Genomes African Sub 1322 A=0.6180 G=0.3820
1000Genomes East Asian Sub 1008 A=0.7927 G=0.2073
1000Genomes Europe Sub 1006 A=0.8976 G=0.1024
1000Genomes South Asian Sub 978 A=0.922 G=0.078
1000Genomes American Sub 694 A=0.898 G=0.102
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9205 G=0.0795
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9094 G=0.0906
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9072 G=0.0928
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7594 G=0.2406
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.919 G=0.081
Northern Sweden ACPOP Study-wide 600 A=0.897 G=0.103
Qatari Global Study-wide 216 A=0.782 G=0.218
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.840 G=0.160
SGDP_PRJ Global Study-wide 178 A=0.416 G=0.584
The Danish reference pan genome Danish Study-wide 40 A=0.90 G=0.10
Siberian Global Study-wide 18 A=0.50 G=0.50
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 2 NC_000002.12:g.241083611A>G
GRCh37.p13 chr 2 NC_000002.11:g.242023026A>G
Gene: SNED1, sushi, nidogen and EGF like domains 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNED1 transcript NM_001080437.3:c.4121+124…

NM_001080437.3:c.4121+1247A>G

N/A Intron Variant
SNED1 transcript variant X2 XM_011510931.3:c.4193+124…

XM_011510931.3:c.4193+1247A>G

N/A Intron Variant
SNED1 transcript variant X7 XM_011510932.3:c.4094+124…

XM_011510932.3:c.4094+1247A>G

N/A Intron Variant
SNED1 transcript variant X3 XM_047443884.1:c.4193+124…

XM_047443884.1:c.4193+1247A>G

N/A Intron Variant
SNED1 transcript variant X8 XM_047443885.1:c.4079+124…

XM_047443885.1:c.4079+1247A>G

N/A Intron Variant
SNED1 transcript variant X10 XM_047443886.1:c.4022+124…

XM_047443886.1:c.4022+1247A>G

N/A Intron Variant
SNED1 transcript variant X11 XM_047443887.1:c.4007+124…

XM_047443887.1:c.4007+1247A>G

N/A Intron Variant
SNED1 transcript variant X12 XM_047443888.1:c.3980+124…

XM_047443888.1:c.3980+1247A>G

N/A Intron Variant
SNED1 transcript variant X14 XM_047443889.1:c.3908+124…

XM_047443889.1:c.3908+1247A>G

N/A Intron Variant
SNED1 transcript variant X15 XM_011510934.4:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X22 XM_011510937.3:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X13 XM_024452784.2:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X19 XM_047443890.1:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X20 XM_047443891.1:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X1 XR_002959254.2:n. N/A Intron Variant
SNED1 transcript variant X4 XR_002959255.2:n. N/A Intron Variant
SNED1 transcript variant X5 XR_002959256.2:n. N/A Intron Variant
SNED1 transcript variant X6 XR_002959257.2:n. N/A Intron Variant
SNED1 transcript variant X9 XR_002959258.2:n. N/A Intron Variant
SNED1 transcript variant X18 XR_002959260.2:n. N/A Intron Variant
SNED1 transcript variant X16 XR_002959262.2:n. N/A Intron Variant
SNED1 transcript variant X21 XR_002959263.2:n. N/A Intron Variant
SNED1 transcript variant X17 XR_007071512.1:n. N/A Intron Variant
Gene: MTERF4, mitochondrial transcription termination factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MTERF4 transcript variant 5 NM_001330179.2:c. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 6 NM_001330180.2:c. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 1 NM_182501.4:c. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 7 NR_138463.2:n. N/A Intron Variant
MTERF4 transcript variant 2 NR_028049.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 3 NR_028050.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 4 NR_028051.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 8 NR_138464.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 9 NR_138465.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 10 NR_138466.2:n. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant X1 XM_047443427.1:c.*160+557…

XM_047443427.1:c.*160+5577T>C

N/A Intron Variant
MTERF4 transcript variant X2 XM_047443428.1:c.*160+557…

XM_047443428.1:c.*160+5577T>C

N/A Intron Variant
MTERF4 transcript variant X3 XM_047443429.1:c. N/A Genic Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G
GRCh38.p14 chr 2 NC_000002.12:g.241083611= NC_000002.12:g.241083611A>G
GRCh37.p13 chr 2 NC_000002.11:g.242023026= NC_000002.11:g.242023026A>G
SNED1 transcript NM_001080437.1:c.4121+1247= NM_001080437.1:c.4121+1247A>G
SNED1 transcript NM_001080437.3:c.4121+1247= NM_001080437.3:c.4121+1247A>G
SNED1 transcript variant X1 XM_005246997.1:c.4121+1247= XM_005246997.1:c.4121+1247A>G
SNED1 transcript variant X2 XM_005246998.1:c.4121+1247= XM_005246998.1:c.4121+1247A>G
SNED1 transcript variant X2 XM_011510931.3:c.4193+1247= XM_011510931.3:c.4193+1247A>G
SNED1 transcript variant X7 XM_011510932.3:c.4094+1247= XM_011510932.3:c.4094+1247A>G
MTERF4 transcript variant X1 XM_047443427.1:c.*160+5577= XM_047443427.1:c.*160+5577T>C
MTERF4 transcript variant X2 XM_047443428.1:c.*160+5577= XM_047443428.1:c.*160+5577T>C
SNED1 transcript variant X3 XM_047443884.1:c.4193+1247= XM_047443884.1:c.4193+1247A>G
SNED1 transcript variant X8 XM_047443885.1:c.4079+1247= XM_047443885.1:c.4079+1247A>G
SNED1 transcript variant X10 XM_047443886.1:c.4022+1247= XM_047443886.1:c.4022+1247A>G
SNED1 transcript variant X11 XM_047443887.1:c.4007+1247= XM_047443887.1:c.4007+1247A>G
SNED1 transcript variant X12 XM_047443888.1:c.3980+1247= XM_047443888.1:c.3980+1247A>G
SNED1 transcript variant X14 XM_047443889.1:c.3908+1247= XM_047443889.1:c.3908+1247A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

60 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11475920 Jul 11, 2003 (116)
2 WUGSC_SSAHASNP ss14468187 Dec 05, 2003 (119)
3 BCMHGSC_JDW ss91608778 Mar 24, 2008 (129)
4 BGI ss103709661 Dec 01, 2009 (131)
5 1000GENOMES ss111065327 Jan 25, 2009 (130)
6 1000GENOMES ss111918979 Jan 25, 2009 (130)
7 ENSEMBL ss138660801 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss165809438 Jul 04, 2010 (132)
9 BUSHMAN ss201979505 Jul 04, 2010 (132)
10 1000GENOMES ss219918281 Jul 14, 2010 (132)
11 1000GENOMES ss231661749 Jul 14, 2010 (132)
12 1000GENOMES ss239104971 Jul 15, 2010 (132)
13 GMI ss276967009 May 04, 2012 (137)
14 PJP ss292522194 May 09, 2011 (134)
15 TISHKOFF ss556349721 Apr 25, 2013 (138)
16 SSMP ss650010839 Apr 25, 2013 (138)
17 EVA-GONL ss978154510 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1070084597 Aug 21, 2014 (142)
19 1000GENOMES ss1302373847 Aug 21, 2014 (142)
20 EVA_GENOME_DK ss1579399143 Apr 01, 2015 (144)
21 EVA_DECODE ss1587613626 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1606188374 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1649182407 Apr 01, 2015 (144)
24 HAMMER_LAB ss1798678050 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1921405225 Feb 12, 2016 (147)
26 JJLAB ss2021251253 Sep 14, 2016 (149)
27 USC_VALOUEV ss2149319343 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2240647225 Dec 20, 2016 (150)
29 GRF ss2703975295 Nov 08, 2017 (151)
30 GNOMAD ss2788360202 Nov 08, 2017 (151)
31 SWEGEN ss2991654788 Nov 08, 2017 (151)
32 BIOINF_KMB_FNS_UNIBA ss3024386757 Nov 08, 2017 (151)
33 CSHL ss3344829009 Nov 08, 2017 (151)
34 EGCUT_WGS ss3659553663 Jul 13, 2019 (153)
35 EVA_DECODE ss3706387203 Jul 13, 2019 (153)
36 ACPOP ss3729535562 Jul 13, 2019 (153)
37 EVA ss3758314895 Jul 13, 2019 (153)
38 PACBIO ss3784203464 Jul 13, 2019 (153)
39 PACBIO ss3789735191 Jul 13, 2019 (153)
40 PACBIO ss3794608831 Jul 13, 2019 (153)
41 KHV_HUMAN_GENOMES ss3802674735 Jul 13, 2019 (153)
42 EVA ss3827602884 Apr 25, 2020 (154)
43 EVA ss3837221638 Apr 25, 2020 (154)
44 EVA ss3842644757 Apr 25, 2020 (154)
45 SGDP_PRJ ss3854987027 Apr 25, 2020 (154)
46 KRGDB ss3900746911 Apr 25, 2020 (154)
47 TOPMED ss4550738516 Apr 27, 2021 (155)
48 TOMMO_GENOMICS ss5157324550 Apr 27, 2021 (155)
49 1000G_HIGH_COVERAGE ss5252673677 Oct 13, 2022 (156)
50 EVA ss5337212590 Oct 13, 2022 (156)
51 HUGCELL_USP ss5452220342 Oct 13, 2022 (156)
52 EVA ss5506853182 Oct 13, 2022 (156)
53 1000G_HIGH_COVERAGE ss5530325392 Oct 13, 2022 (156)
54 SANFORD_IMAGENETICS ss5631319514 Oct 13, 2022 (156)
55 TOMMO_GENOMICS ss5688458947 Oct 13, 2022 (156)
56 YY_MCH ss5803383154 Oct 13, 2022 (156)
57 EVA ss5821846395 Oct 13, 2022 (156)
58 EVA ss5853030028 Oct 13, 2022 (156)
59 EVA ss5935445191 Oct 13, 2022 (156)
60 EVA ss5957589797 Oct 13, 2022 (156)
61 1000Genomes NC_000002.11 - 242023026 Oct 11, 2018 (152)
62 1000Genomes_30x NC_000002.12 - 241083611 Oct 13, 2022 (156)
63 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 242023026 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000002.11 - 242023026 Oct 11, 2018 (152)
65 The Danish reference pan genome NC_000002.11 - 242023026 Apr 25, 2020 (154)
66 gnomAD - Genomes NC_000002.12 - 241083611 Apr 27, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000002.11 - 242023026 Apr 25, 2020 (154)
68 KOREAN population from KRGDB NC_000002.11 - 242023026 Apr 25, 2020 (154)
69 Northern Sweden NC_000002.11 - 242023026 Jul 13, 2019 (153)
70 Qatari NC_000002.11 - 242023026 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000002.11 - 242023026 Apr 25, 2020 (154)
72 Siberian NC_000002.11 - 242023026 Apr 25, 2020 (154)
73 8.3KJPN NC_000002.11 - 242023026 Apr 27, 2021 (155)
74 14KJPN NC_000002.12 - 241083611 Oct 13, 2022 (156)
75 TopMed NC_000002.12 - 241083611 Apr 27, 2021 (155)
76 UK 10K study - Twins NC_000002.11 - 242023026 Oct 11, 2018 (152)
77 A Vietnamese Genetic Variation Database NC_000002.11 - 242023026 Jul 13, 2019 (153)
78 ALFA NC_000002.12 - 241083611 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91608778, ss111065327, ss111918979, ss165809438, ss201979505, ss276967009, ss292522194, ss1587613626 NC_000002.10:241671698:A:G NC_000002.12:241083610:A:G (self)
13504835, 7485434, 5291911, 5564082, 3280868, 7924305, 2820427, 3447155, 7004007, 1835697, 15293857, 7485434, 1626314, ss219918281, ss231661749, ss239104971, ss556349721, ss650010839, ss978154510, ss1070084597, ss1302373847, ss1579399143, ss1606188374, ss1649182407, ss1798678050, ss1921405225, ss2021251253, ss2149319343, ss2703975295, ss2788360202, ss2991654788, ss3344829009, ss3659553663, ss3729535562, ss3758314895, ss3784203464, ss3789735191, ss3794608831, ss3827602884, ss3837221638, ss3854987027, ss3900746911, ss5157324550, ss5337212590, ss5506853182, ss5631319514, ss5821846395, ss5957589797 NC_000002.11:242023025:A:G NC_000002.12:241083610:A:G (self)
17851327, 96083959, 22296051, 354561395, 3878752842, ss2240647225, ss3024386757, ss3706387203, ss3802674735, ss3842644757, ss4550738516, ss5252673677, ss5452220342, ss5530325392, ss5688458947, ss5803383154, ss5853030028, ss5935445191 NC_000002.12:241083610:A:G NC_000002.12:241083610:A:G (self)
ss11475920 NT_005416.10:1193005:A:G NC_000002.12:241083610:A:G (self)
ss14468187 NT_005416.11:1197629:A:G NC_000002.12:241083610:A:G (self)
ss103709661, ss138660801 NT_005416.13:1213893:A:G NC_000002.12:241083610:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs7580472

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07