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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.

rs4246500

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:877371 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.084125 (22267/264690, TOPMED)
T=0.080661 (11303/140130, GnomAD)
T=0.04463 (843/18890, ALFA) (+ 12 more)
T=0.07041 (1180/16760, 8.3KJPN)
T=0.0807 (404/5008, 1000G)
T=0.0010 (4/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.0078 (23/2930, KOREAN)
T=0.0076 (14/1832, Korea1K)
T=0.002 (1/600, NorthernSweden)
T=0.033 (18/548, SGDP_PRJ)
T=0.051 (11/216, Qatari)
T=0.000 (0/212, Vietnamese)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FAM41C : 2KB Upstream 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.877371T>A
GRCh38.p13 chr 1 NC_000001.11:g.877371T>C
GRCh38.p13 chr 1 NC_000001.11:g.877371T>G
GRCh37.p13 chr 1 NC_000001.10:g.812751T>A
GRCh37.p13 chr 1 NC_000001.10:g.812751T>C
GRCh37.p13 chr 1 NC_000001.10:g.812751T>G
Gene: FAM41C, family with sequence similarity 41 member C (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
FAM41C transcript NR_027055.1:n. N/A Upstream 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

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 18890 T=0.04463 C=0.95537
European Sub 14286 T=0.00091 C=0.99909
African Sub 2946 T=0.2576 C=0.7424
African Others Sub 114 T=0.254 C=0.746
African American Sub 2832 T=0.2578 C=0.7422
Asian Sub 112 T=0.009 C=0.991
East Asian Sub 86 T=0.01 C=0.99
Other Asian Sub 26 T=0.00 C=1.00
Latin American 1 Sub 146 T=0.096 C=0.904
Latin American 2 Sub 610 T=0.016 C=0.984
South Asian Sub 98 T=0.00 C=1.00
Other Sub 692 T=0.066 C=0.934


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 T=0.084125 C=0.915875
gnomAD - Genomes Global Study-wide 140130 T=0.080661 C=0.919339
gnomAD - Genomes European Sub 75950 T=0.00126 C=0.99874
gnomAD - Genomes African Sub 41914 T=0.25280 C=0.74720
gnomAD - Genomes American Sub 13656 T=0.03251 C=0.96749
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.0015 C=0.9985
gnomAD - Genomes East Asian Sub 3132 T=0.0051 C=0.9949
gnomAD - Genomes Other Sub 2154 T=0.0678 C=0.9322
8.3KJPN JAPANESE Study-wide 16760 T=0.07041 C=0.92959
1000Genomes Global Study-wide 5008 T=0.0807 C=0.9193
1000Genomes African Sub 1322 T=0.2806 C=0.7194
1000Genomes East Asian Sub 1008 T=0.0159 C=0.9841
1000Genomes Europe Sub 1006 T=0.0020 C=0.9980
1000Genomes South Asian Sub 978 T=0.000 C=1.000
1000Genomes American Sub 694 T=0.022 C=0.978
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.0010 C=0.9990
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.0003 C=0.9997
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0078 A=0.0000, C=0.9922, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.0076 C=0.9924
Northern Sweden ACPOP Study-wide 600 T=0.002 C=0.998
SGDP_PRJ Global Study-wide 548 T=0.033 C=0.967
Qatari Global Study-wide 216 T=0.051 C=0.949
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.000 C=1.000
Siberian Global Study-wide 56 T=0.00 C=1.00
The Danish reference pan genome Danish Study-wide 40 T=0.00 C=1.00
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 G
GRCh38.p13 chr 1 NC_000001.11:g.877371= NC_000001.11:g.877371T>A NC_000001.11:g.877371T>C NC_000001.11:g.877371T>G
GRCh37.p13 chr 1 NC_000001.10:g.812751= NC_000001.10:g.812751T>A NC_000001.10:g.812751T>C NC_000001.10:g.812751T>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, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6186664 Feb 20, 2003 (111)
2 WI_SSAHASNP ss6879531 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9853067 Jul 11, 2003 (116)
4 WI_SSAHASNP ss11382837 Jul 11, 2003 (116)
5 SSAHASNP ss22883269 Apr 05, 2004 (121)
6 HGSV ss77156532 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss87156240 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97913290 Feb 04, 2009 (130)
9 BGI ss105111749 Dec 01, 2009 (131)
10 1000GENOMES ss107938303 Jan 22, 2009 (130)
11 ILLUMINA-UK ss118438492 Feb 14, 2009 (130)
12 ENSEMBL ss137752391 Dec 01, 2009 (131)
13 ENSEMBL ss138885704 Dec 01, 2009 (131)
14 GMI ss154522515 Dec 01, 2009 (131)
15 BUSHMAN ss197885575 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss205402018 Jul 04, 2010 (132)
17 1000GENOMES ss218190514 Jul 14, 2010 (132)
18 1000GENOMES ss230395532 Jul 14, 2010 (132)
19 1000GENOMES ss238115049 Jul 15, 2010 (132)
20 BL ss252864240 May 09, 2011 (134)
21 GMI ss275681029 May 04, 2012 (137)
22 GMI ss283987440 Apr 25, 2013 (138)
23 PJP ss290493855 May 09, 2011 (134)
24 SSMP ss647516547 Apr 25, 2013 (138)
25 JMKIDD_LAB ss1067612480 Aug 21, 2014 (142)
26 1000GENOMES ss1289340704 Aug 21, 2014 (142)
27 DDI ss1425684997 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1573851253 Apr 01, 2015 (144)
29 EVA_DECODE ss1584129708 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1599378654 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1642372687 Apr 01, 2015 (144)
32 HAMMER_LAB ss1793706318 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1917960971 Feb 12, 2016 (147)
34 GENOMED ss1966667374 Jul 19, 2016 (147)
35 JJLAB ss2019498536 Sep 14, 2016 (149)
36 USC_VALOUEV ss2147484552 Dec 20, 2016 (150)
37 TOPMED ss2321505951 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624264845 Nov 08, 2017 (151)
39 GRF ss2697374982 Nov 08, 2017 (151)
40 GNOMAD ss2750643028 Nov 08, 2017 (151)
41 SWEGEN ss2986149706 Nov 08, 2017 (151)
42 TOPMED ss3066409024 Nov 08, 2017 (151)
43 CSHL ss3343272802 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3645022415 Oct 11, 2018 (152)
45 URBANLAB ss3646581283 Oct 11, 2018 (152)
46 EVA_DECODE ss3685992707 Jul 12, 2019 (153)
47 ACPOP ss3726716604 Jul 12, 2019 (153)
48 EVA ss3745721325 Jul 12, 2019 (153)
49 PACBIO ss3783302223 Jul 12, 2019 (153)
50 PACBIO ss3788980102 Jul 12, 2019 (153)
51 PACBIO ss3793852636 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3798744013 Jul 12, 2019 (153)
53 EVA ss3825981548 Apr 25, 2020 (154)
54 EVA ss3836378492 Apr 25, 2020 (154)
55 EVA ss3841782497 Apr 25, 2020 (154)
56 SGDP_PRJ ss3847996672 Apr 25, 2020 (154)
57 KRGDB ss3892837014 Apr 25, 2020 (154)
58 KOGIC ss3943630401 Apr 25, 2020 (154)
59 TOPMED ss4436443287 Apr 25, 2021 (155)
60 TOMMO_GENOMICS ss5142054123 Apr 25, 2021 (155)
61 1000Genomes NC_000001.10 - 812751 Oct 11, 2018 (152)
62 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 812751 Oct 11, 2018 (152)
63 The Danish reference pan genome NC_000001.10 - 812751 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000001.11 - 877371 Apr 25, 2021 (155)
65 KOREAN population from KRGDB NC_000001.10 - 812751 Apr 25, 2020 (154)
66 Korean Genome Project NC_000001.11 - 877371 Apr 25, 2020 (154)
67 Northern Sweden NC_000001.10 - 812751 Jul 12, 2019 (153)
68 Qatari NC_000001.10 - 812751 Apr 25, 2020 (154)
69 SGDP_PRJ NC_000001.10 - 812751 Apr 25, 2020 (154)
70 Siberian NC_000001.10 - 812751 Apr 25, 2020 (154)
71 8.3KJPN NC_000001.10 - 812751 Apr 25, 2021 (155)
72 TopMed NC_000001.11 - 877371 Apr 25, 2021 (155)
73 UK 10K study - Twins NC_000001.10 - 812751 Oct 11, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000001.10 - 812751 Jul 12, 2019 (153)
75 ALFA NC_000001.11 - 877371 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
14408, ss3892837014 NC_000001.10:812750:T:A NC_000001.11:877370:T:A (self)
ss77156532 NC_000001.8:852613:T:C NC_000001.11:877370:T:C (self)
ss87156240, ss107938303, ss118438492, ss197885575, ss205402018, ss252864240, ss275681029, ss283987440, ss290493855, ss1584129708 NC_000001.9:802613:T:C NC_000001.11:877370:T:C (self)
5486, 638, 1358487, 14408, 1469, 2901, 13652, 906, 23430, 638, 136, ss218190514, ss230395532, ss238115049, ss647516547, ss1067612480, ss1289340704, ss1425684997, ss1573851253, ss1599378654, ss1642372687, ss1793706318, ss1917960971, ss1966667374, ss2019498536, ss2147484552, ss2321505951, ss2624264845, ss2697374982, ss2750643028, ss2986149706, ss3343272802, ss3726716604, ss3745721325, ss3783302223, ss3788980102, ss3793852636, ss3825981548, ss3836378492, ss3847996672, ss3892837014, ss5142054123 NC_000001.10:812750:T:C NC_000001.11:877370:T:C (self)
74145, 8402, 23379, 49622, 7026068013, ss3066409024, ss3645022415, ss3646581283, ss3685992707, ss3798744013, ss3841782497, ss3943630401, ss4436443287 NC_000001.11:877370:T:C NC_000001.11:877370:T:C (self)
ss6186664, ss6879531, ss22883269, ss97913290, ss105111749, ss137752391, ss138885704, ss154522515 NT_004350.19:291382:T:C NC_000001.11:877370:T:C (self)
ss9853067, ss11382837 NT_077982.1:2991:T:C NC_000001.11:877370:T:C (self)
14408, ss3892837014 NC_000001.10:812750:T:G NC_000001.11:877370:T: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 rs4246500

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