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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.

rs72631880

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:870176 (GRCh38.p13) 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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.090795 (12715/140040, GnomAD)
A=0.10734 (8447/78696, PAGE_STUDY)
A=0.03952 (672/17004, ALFA) (+ 13 more)
A=0.28294 (4742/16760, 8.3KJPN)
A=0.1733 (868/5008, 1000G)
A=0.0825 (318/3854, ALSPAC)
A=0.0860 (319/3708, TWINSUK)
A=0.3170 (927/2924, KOREAN)
A=0.3150 (577/1832, Korea1K)
A=0.083 (50/600, NorthernSweden)
A=0.157 (34/216, Qatari)
A=0.229 (49/214, Vietnamese)
T=0.438 (57/130, SGDP_PRJ)
A=0.07 (3/40, GENOME_DK)
T=0.5 (4/8, Siberian)
A=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FAM41C : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.870176T>A
GRCh38.p13 chr 1 NC_000001.11:g.870176T>C
GRCh37.p13 chr 1 NC_000001.10:g.805556T>A
GRCh37.p13 chr 1 NC_000001.10:g.805556T>C
Gene: FAM41C, family with sequence similarity 41 member C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FAM41C transcript NR_027055.1:n. N/A Intron 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 17004 T=0.96048 A=0.03952, C=0.00000
European Sub 13040 T=0.95222 A=0.04778, C=0.00000
African Sub 2622 T=0.9874 A=0.0126, C=0.0000
African Others Sub 102 T=0.990 A=0.010, C=0.000
African American Sub 2520 T=0.9873 A=0.0127, C=0.0000
Asian Sub 54 T=1.00 A=0.00, C=0.00
East Asian Sub 40 T=1.00 A=0.00, C=0.00
Other Asian Sub 14 T=1.00 A=0.00, C=0.00
Latin American 1 Sub 120 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 536 T=1.000 A=0.000, C=0.000
South Asian Sub 44 T=1.00 A=0.00, C=0.00
Other Sub 588 T=0.973 A=0.027, C=0.000


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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 140040 T=0.909205 A=0.090795
gnomAD - Genomes European Sub 75810 T=0.90774 A=0.09226
gnomAD - Genomes African Sub 42000 T=0.93052 A=0.06948
gnomAD - Genomes American Sub 13658 T=0.90804 A=0.09196
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.9011 A=0.0989
gnomAD - Genomes East Asian Sub 3104 T=0.6778 A=0.3222
gnomAD - Genomes Other Sub 2150 T=0.8981 A=0.1019
The PAGE Study Global Study-wide 78696 T=0.89266 A=0.10734
The PAGE Study AfricanAmerican Sub 32514 T=0.93058 A=0.06942
The PAGE Study Mexican Sub 10808 T=0.93866 A=0.06134
The PAGE Study Asian Sub 8318 T=0.7000 A=0.3000
The PAGE Study PuertoRican Sub 7918 T=0.9285 A=0.0715
The PAGE Study NativeHawaiian Sub 4534 T=0.7525 A=0.2475
The PAGE Study Cuban Sub 4228 T=0.9163 A=0.0837
The PAGE Study Dominican Sub 3828 T=0.9185 A=0.0815
The PAGE Study CentralAmerican Sub 2450 T=0.9269 A=0.0731
The PAGE Study SouthAmerican Sub 1982 T=0.9147 A=0.0853
The PAGE Study NativeAmerican Sub 1260 T=0.9310 A=0.0690
The PAGE Study SouthAsian Sub 856 T=0.716 A=0.284
8.3KJPN JAPANESE Study-wide 16760 T=0.71706 A=0.28294
1000Genomes Global Study-wide 5008 T=0.8267 A=0.1733
1000Genomes African Sub 1322 T=0.9145 A=0.0855
1000Genomes East Asian Sub 1008 T=0.6825 A=0.3175
1000Genomes Europe Sub 1006 T=0.9076 A=0.0924
1000Genomes South Asian Sub 978 T=0.706 A=0.294
1000Genomes American Sub 694 T=0.922 A=0.078
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9175 A=0.0825
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9140 A=0.0860
KOREAN population from KRGDB KOREAN Study-wide 2924 T=0.6830 A=0.3170
Korean Genome Project KOREAN Study-wide 1832 T=0.6850 A=0.3150
Northern Sweden ACPOP Study-wide 600 T=0.917 A=0.083
Qatari Global Study-wide 216 T=0.843 A=0.157
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.771 A=0.229
SGDP_PRJ Global Study-wide 130 T=0.438 A=0.562
The Danish reference pan genome Danish Study-wide 40 T=0.93 A=0.07
Siberian Global Study-wide 8 T=0.5 A=0.5
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 T= A C
GRCh38.p13 chr 1 NC_000001.11:g.870176= NC_000001.11:g.870176T>A NC_000001.11:g.870176T>C
GRCh37.p13 chr 1 NC_000001.10:g.805556= NC_000001.10:g.805556T>A NC_000001.10:g.805556T>C
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#.

39 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss107938295 Feb 13, 2009 (130)
2 COMPLETE_GENOMICS ss165981079 Jul 04, 2010 (132)
3 1000GENOMES ss238115031 Jul 15, 2010 (132)
4 TISHKOFF ss553710683 Apr 25, 2013 (138)
5 SSMP ss647516508 Apr 25, 2013 (138)
6 EVA-GONL ss974769662 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1067612451 Aug 21, 2014 (142)
8 1000GENOMES ss1289340481 Aug 21, 2014 (142)
9 DDI ss1425684979 Apr 01, 2015 (144)
10 EVA_GENOME_DK ss1573851234 Apr 01, 2015 (144)
11 EVA_DECODE ss1584129675 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1599378599 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1642372632 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1917960864 Feb 12, 2016 (147)
15 ILLUMINA ss1958229997 Feb 12, 2016 (147)
16 JJLAB ss2019498516 Sep 14, 2016 (149)
17 USC_VALOUEV ss2147484491 Dec 20, 2016 (150)
18 TOPMED ss2321505576 Dec 20, 2016 (150)
19 SYSTEMSBIOZJU ss2624264835 Nov 08, 2017 (151)
20 GRF ss2697374929 Nov 08, 2017 (151)
21 GNOMAD ss2750642257 Nov 08, 2017 (151)
22 SWEGEN ss2986149581 Nov 08, 2017 (151)
23 ILLUMINA ss3021043028 Nov 08, 2017 (151)
24 BIOINF_KMB_FNS_UNIBA ss3023513723 Nov 08, 2017 (151)
25 TOPMED ss3066407426 Nov 08, 2017 (151)
26 CSHL ss3343272746 Nov 08, 2017 (151)
27 ILLUMINA ss3651365079 Oct 11, 2018 (152)
28 EVA_DECODE ss3685992583 Jul 12, 2019 (153)
29 ILLUMINA ss3724988063 Jul 12, 2019 (153)
30 ACPOP ss3726716569 Jul 12, 2019 (153)
31 EVA ss3745721254 Jul 12, 2019 (153)
32 PAGE_CC ss3770778534 Jul 12, 2019 (153)
33 KHV_HUMAN_GENOMES ss3798743943 Jul 12, 2019 (153)
34 SGDP_PRJ ss3847996315 Apr 25, 2020 (154)
35 KRGDB ss3892836614 Apr 25, 2020 (154)
36 KOGIC ss3943630221 Apr 25, 2020 (154)
37 TOPMED ss4436441732 Apr 25, 2021 (155)
38 TOPMED ss4436441733 Apr 25, 2021 (155)
39 TOMMO_GENOMICS ss5142053674 Apr 25, 2021 (155)
40 1000Genomes NC_000001.10 - 805556 Oct 11, 2018 (152)
41 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 805556 Oct 11, 2018 (152)
42 The Danish reference pan genome NC_000001.10 - 805556 Apr 25, 2020 (154)
43 gnomAD - Genomes NC_000001.11 - 870176 Apr 25, 2021 (155)
44 KOREAN population from KRGDB NC_000001.10 - 805556 Apr 25, 2020 (154)
45 Korean Genome Project NC_000001.11 - 870176 Apr 25, 2020 (154)
46 Northern Sweden NC_000001.10 - 805556 Jul 12, 2019 (153)
47 The PAGE Study NC_000001.11 - 870176 Jul 12, 2019 (153)
48 Qatari NC_000001.10 - 805556 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000001.10 - 805556 Apr 25, 2020 (154)
50 Siberian NC_000001.10 - 805556 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 805556 Apr 25, 2021 (155)
52 TopMed

Submission ignored due to conflicting rows:
Row 48067 (NC_000001.11:870175:T:A 24459/264690)
Row 48068 (NC_000001.11:870175:T:C 1/264690)

- Apr 25, 2021 (155)
53 TopMed

Submission ignored due to conflicting rows:
Row 48067 (NC_000001.11:870175:T:A 24459/264690)
Row 48068 (NC_000001.11:870175:T:C 1/264690)

- Apr 25, 2021 (155)
54 UK 10K study - Twins NC_000001.10 - 805556 Oct 11, 2018 (152)
55 A Vietnamese Genetic Variation Database NC_000001.10 - 805556 Jul 12, 2019 (153)
56 ALFA NC_000001.11 - 870176 Apr 25, 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
ss107938295, ss165981079, ss1584129675 NC_000001.9:795418:T:A NC_000001.11:870175:T:A (self)
5258, 572, 1358468, 14008, 1434, 2794, 13295, 845, 22981, 572, 120, ss238115031, ss553710683, ss647516508, ss974769662, ss1067612451, ss1289340481, ss1425684979, ss1573851234, ss1599378599, ss1642372632, ss1917960864, ss1958229997, ss2019498516, ss2147484491, ss2321505576, ss2624264835, ss2697374929, ss2750642257, ss2986149581, ss3021043028, ss3343272746, ss3651365079, ss3726716569, ss3745721254, ss3847996315, ss3892836614, ss5142053674 NC_000001.10:805555:T:A NC_000001.11:870175:T:A (self)
72712, 8222, 3, 22410, 8783465504, ss3023513723, ss3066407426, ss3685992583, ss3724988063, ss3770778534, ss3798743943, ss3943630221, ss4436441732 NC_000001.11:870175:T:A NC_000001.11:870175:T:A (self)
8783465504, ss4436441733 NC_000001.11:870175:T:C NC_000001.11:870175:T:C
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 rs72631880

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.post596+ae089ad