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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs139310992

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:1383936 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.001160 (307/264690, TOPMED)
A=0.000305 (75/246302, GnomAD_exome)
A=0.001034 (145/140224, GnomAD) (+ 8 more)
A=0.000204 (23/112472, ALFA)
A=0.000310 (33/106476, ExAC)
A=0.00177 (139/78642, PAGE_STUDY)
A=0.00131 (17/13002, GO-ESP)
A=0.0009 (6/6404, 1000G_30x)
A=0.0008 (4/5008, 1000G)
A=0.0003 (1/2920, KOREAN)
A=0.0005 (1/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UVSSA : Missense 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 112594 G=0.999796 A=0.000204
European Sub 93450 G=0.99995 A=0.00005
African Sub 4148 G=0.9969 A=0.0031
African Others Sub 124 G=1.000 A=0.000
African American Sub 4024 G=0.9968 A=0.0032
Asian Sub 3188 G=0.9997 A=0.0003
East Asian Sub 1940 G=0.9995 A=0.0005
Other Asian Sub 1248 G=1.0000 A=0.0000
Latin American 1 Sub 152 G=1.000 A=0.000
Latin American 2 Sub 632 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 10920 G=0.99963 A=0.00037


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 G=0.998840 A=0.001160
gnomAD - Exomes Global Study-wide 246302 G=0.999695 A=0.000305
gnomAD - Exomes European Sub 131680 G=0.999977 A=0.000023
gnomAD - Exomes Asian Sub 48684 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 34228 G=0.99985 A=0.00015
gnomAD - Exomes African Sub 15800 G=0.99595 A=0.00405
gnomAD - Exomes Ashkenazi Jewish Sub 9876 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6034 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140224 G=0.998966 A=0.001034
gnomAD - Genomes European Sub 75928 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 42032 G=0.99672 A=0.00328
gnomAD - Genomes American Sub 13662 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9981 A=0.0019
Allele Frequency Aggregator Total Global 112472 G=0.999796 A=0.000204
Allele Frequency Aggregator European Sub 93346 G=0.99995 A=0.00005
Allele Frequency Aggregator Other Sub 10916 G=0.99963 A=0.00037
Allele Frequency Aggregator African Sub 4134 G=0.9969 A=0.0031
Allele Frequency Aggregator Asian Sub 3188 G=0.9997 A=0.0003
Allele Frequency Aggregator Latin American 2 Sub 632 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 152 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
ExAC Global Study-wide 106476 G=0.999690 A=0.000310
ExAC Europe Sub 63380 G=0.99997 A=0.00003
ExAC Asian Sub 23146 G=0.99996 A=0.00004
ExAC American Sub 10322 G=0.99990 A=0.00010
ExAC African Sub 8854 G=0.9967 A=0.0033
ExAC Other Sub 774 G=1.000 A=0.000
The PAGE Study Global Study-wide 78642 G=0.99823 A=0.00177
The PAGE Study AfricanAmerican Sub 32468 G=0.99646 A=0.00354
The PAGE Study Mexican Sub 10808 G=0.99981 A=0.00019
The PAGE Study Asian Sub 8314 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7914 G=0.9989 A=0.0011
The PAGE Study NativeHawaiian Sub 4532 G=0.9996 A=0.0004
The PAGE Study Cuban Sub 4230 G=0.9998 A=0.0002
The PAGE Study Dominican Sub 3828 G=0.9979 A=0.0021
The PAGE Study CentralAmerican Sub 2450 G=0.9992 A=0.0008
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13002 G=0.99869 A=0.00131
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4402 G=0.9961 A=0.0039
1000Genomes_30x Global Study-wide 6404 G=0.9991 A=0.0009
1000Genomes_30x African Sub 1786 G=0.9978 A=0.0022
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.998 A=0.002
1000Genomes Global Study-wide 5008 G=0.9992 A=0.0008
1000Genomes African Sub 1322 G=0.9977 A=0.0023
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9997 A=0.0003
Korean Genome Project KOREAN Study-wide 1832 G=0.9995 A=0.0005
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 4 NC_000004.12:g.1383936G>A
GRCh37.p13 chr 4 NC_000004.11:g.1377724G>A
UVSSA RefSeqGene NG_032753.1:g.41621G>A
Gene: UVSSA, UV stimulated scaffold protein A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
UVSSA transcript variant 1 NM_020894.4:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A NP_065945.2:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant 2 NM_001317934.2:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A NP_001304863.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant 3 NM_001317935.2:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A NP_001304864.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X10 XM_017008496.2:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X15 XM_017008497.3:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X16 XM_017008498.3:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X17 XM_017008499.2:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X3 XM_047416025.1:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X4 XM_047416026.1:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X18 XM_047416028.1:c. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X6 XM_017008490.1:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X2 XP_016863979.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X19 XM_017008500.1:c.862G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X10 XP_016863989.1:p.Ala288Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X9 XM_017008495.2:c.1744G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X3 XP_016863984.1:p.Ala582Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X5 XM_017008492.3:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X2 XP_016863981.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X7 XM_017008494.3:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X2 XP_016863983.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X8 XM_017008493.3:c.2032G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X2 XP_016863982.1:p.Ala678Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X14 XM_047416027.1:c.1690G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X5 XP_047271983.1:p.Ala564Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X20 XM_024454162.2:c.685G>A A [GCC] > T [ACC] Coding Sequence Variant
UV-stimulated scaffold protein A isoform X11 XP_024309930.1:p.Ala229Thr A (Ala) > T (Thr) Missense Variant
UVSSA transcript variant X1 XR_007057948.1:n.2295G>A N/A Non Coding Transcript Variant
UVSSA transcript variant X2 XR_007057949.1:n.2295G>A N/A Non Coding Transcript Variant
UVSSA transcript variant X12 XR_001741302.2:n. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X11 XR_001741303.2:n. N/A Genic Downstream Transcript Variant
UVSSA transcript variant X13 XR_001741304.2:n. 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 G= A
GRCh38.p14 chr 4 NC_000004.12:g.1383936= NC_000004.12:g.1383936G>A
GRCh37.p13 chr 4 NC_000004.11:g.1377724= NC_000004.11:g.1377724G>A
UVSSA RefSeqGene NG_032753.1:g.41621= NG_032753.1:g.41621G>A
UVSSA transcript variant 1 NM_020894.4:c.2032= NM_020894.4:c.2032G>A
UVSSA transcript variant 1 NM_020894.3:c.2032= NM_020894.3:c.2032G>A
UVSSA transcript NM_020894.2:c.2032= NM_020894.2:c.2032G>A
UVSSA transcript variant 3 NM_001317935.2:c.2032= NM_001317935.2:c.2032G>A
UVSSA transcript variant 3 NM_001317935.1:c.2032= NM_001317935.1:c.2032G>A
UVSSA transcript variant 2 NM_001317934.2:c.2032= NM_001317934.2:c.2032G>A
UVSSA transcript variant 2 NM_001317934.1:c.2032= NM_001317934.1:c.2032G>A
UVSSA transcript variant X8 XM_017008493.3:c.2032= XM_017008493.3:c.2032G>A
UVSSA transcript variant X7 XM_017008493.2:c.2032= XM_017008493.2:c.2032G>A
UVSSA transcript variant X8 XM_017008493.1:c.2032= XM_017008493.1:c.2032G>A
UVSSA transcript variant X5 XM_017008492.3:c.2032= XM_017008492.3:c.2032G>A
UVSSA transcript variant X8 XM_017008492.2:c.2032= XM_017008492.2:c.2032G>A
UVSSA transcript variant X7 XM_017008492.1:c.2032= XM_017008492.1:c.2032G>A
UVSSA transcript variant X7 XM_017008494.3:c.2032= XM_017008494.3:c.2032G>A
UVSSA transcript variant X9 XM_017008494.2:c.2032= XM_017008494.2:c.2032G>A
UVSSA transcript variant X9 XM_017008494.1:c.2032= XM_017008494.1:c.2032G>A
UVSSA transcript variant X9 XM_017008495.2:c.1744= XM_017008495.2:c.1744G>A
UVSSA transcript variant X10 XM_017008495.1:c.1744= XM_017008495.1:c.1744G>A
UVSSA transcript variant X20 XM_024454162.2:c.685= XM_024454162.2:c.685G>A
UVSSA transcript variant X20 XM_024454162.1:c.685= XM_024454162.1:c.685G>A
UVSSA transcript variant X1 XR_007057948.1:n.2295= XR_007057948.1:n.2295G>A
UVSSA transcript variant X2 XR_007057949.1:n.2295= XR_007057949.1:n.2295G>A
UVSSA transcript variant X14 XM_047416027.1:c.1690= XM_047416027.1:c.1690G>A
UVSSA transcript variant X6 XM_017008490.1:c.2032= XM_017008490.1:c.2032G>A
UVSSA transcript variant X19 XM_017008500.1:c.862= XM_017008500.1:c.862G>A
UV-stimulated scaffold protein A NP_065945.2:p.Ala678= NP_065945.2:p.Ala678Thr
UV-stimulated scaffold protein A NP_001304864.1:p.Ala678= NP_001304864.1:p.Ala678Thr
UV-stimulated scaffold protein A NP_001304863.1:p.Ala678= NP_001304863.1:p.Ala678Thr
UV-stimulated scaffold protein A isoform X2 XP_016863982.1:p.Ala678= XP_016863982.1:p.Ala678Thr
UV-stimulated scaffold protein A isoform X2 XP_016863981.1:p.Ala678= XP_016863981.1:p.Ala678Thr
UV-stimulated scaffold protein A isoform X2 XP_016863983.1:p.Ala678= XP_016863983.1:p.Ala678Thr
UV-stimulated scaffold protein A isoform X3 XP_016863984.1:p.Ala582= XP_016863984.1:p.Ala582Thr
UV-stimulated scaffold protein A isoform X11 XP_024309930.1:p.Ala229= XP_024309930.1:p.Ala229Thr
UV-stimulated scaffold protein A isoform X5 XP_047271983.1:p.Ala564= XP_047271983.1:p.Ala564Thr
UV-stimulated scaffold protein A isoform X2 XP_016863979.1:p.Ala678= XP_016863979.1:p.Ala678Thr
UV-stimulated scaffold protein A isoform X10 XP_016863989.1:p.Ala288= XP_016863989.1:p.Ala288Thr
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#.

41 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342157188 May 09, 2011 (134)
2 1000GENOMES ss488779621 May 04, 2012 (137)
3 EXOME_CHIP ss491352195 May 04, 2012 (137)
4 ILLUMINA ss780826143 Sep 08, 2015 (146)
5 ILLUMINA ss783508847 Sep 08, 2015 (146)
6 1000GENOMES ss1308080203 Aug 21, 2014 (142)
7 EVA_EXAC ss1687386251 Apr 01, 2015 (144)
8 ILLUMINA ss1752499231 Sep 08, 2015 (146)
9 ILLUMINA ss1917777509 Feb 12, 2016 (147)
10 ILLUMINA ss1946107805 Feb 12, 2016 (147)
11 ILLUMINA ss1958650228 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2259806655 Dec 20, 2016 (150)
13 GNOMAD ss2734341477 Nov 08, 2017 (151)
14 GNOMAD ss2747185161 Nov 08, 2017 (151)
15 GNOMAD ss2804664010 Nov 08, 2017 (151)
16 AFFY ss2985282945 Nov 08, 2017 (151)
17 ILLUMINA ss3022336596 Nov 08, 2017 (151)
18 ILLUMINA ss3628883444 Oct 12, 2018 (152)
19 ILLUMINA ss3634937137 Oct 12, 2018 (152)
20 ILLUMINA ss3640644433 Oct 12, 2018 (152)
21 ILLUMINA ss3644840492 Oct 12, 2018 (152)
22 ILLUMINA ss3652819066 Oct 12, 2018 (152)
23 ILLUMINA ss3654053320 Oct 12, 2018 (152)
24 ILLUMINA ss3726101795 Jul 13, 2019 (153)
25 ILLUMINA ss3744521535 Jul 13, 2019 (153)
26 ILLUMINA ss3745237382 Jul 13, 2019 (153)
27 EVA ss3761282378 Jul 13, 2019 (153)
28 PAGE_CC ss3771099252 Jul 13, 2019 (153)
29 ILLUMINA ss3772732194 Jul 13, 2019 (153)
30 EVA ss3823993374 Apr 25, 2020 (154)
31 KRGDB ss3904145325 Apr 25, 2020 (154)
32 KOGIC ss3953348798 Apr 25, 2020 (154)
33 TOPMED ss4600103040 Apr 25, 2021 (155)
34 1000G_HIGH_COVERAGE ss5257734679 Oct 13, 2022 (156)
35 EVA ss5346358979 Oct 13, 2022 (156)
36 HUGCELL_USP ss5456689752 Oct 13, 2022 (156)
37 1000G_HIGH_COVERAGE ss5538029385 Oct 13, 2022 (156)
38 SANFORD_IMAGENETICS ss5634169462 Oct 13, 2022 (156)
39 EVA ss5847998373 Oct 13, 2022 (156)
40 EVA ss5861807688 Oct 13, 2022 (156)
41 EVA ss5962544924 Oct 13, 2022 (156)
42 1000Genomes NC_000004.11 - 1377724 Oct 12, 2018 (152)
43 1000Genomes_30x NC_000004.12 - 1383936 Oct 13, 2022 (156)
44 ExAC NC_000004.11 - 1377724 Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000004.12 - 1383936 Apr 25, 2021 (155)
46 gnomAD - Exomes NC_000004.11 - 1377724 Jul 13, 2019 (153)
47 GO Exome Sequencing Project NC_000004.11 - 1377724 Oct 12, 2018 (152)
48 KOREAN population from KRGDB NC_000004.11 - 1377724 Apr 25, 2020 (154)
49 Korean Genome Project NC_000004.12 - 1383936 Apr 25, 2020 (154)
50 The PAGE Study NC_000004.12 - 1383936 Jul 13, 2019 (153)
51 TopMed NC_000004.12 - 1383936 Apr 25, 2021 (155)
52 ALFA NC_000004.12 - 1383936 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
19417862, 7341889, 3441215, 451628, 11322719, ss342157188, ss488779621, ss491352195, ss780826143, ss783508847, ss1308080203, ss1687386251, ss1752499231, ss1917777509, ss1946107805, ss1958650228, ss2734341477, ss2747185161, ss2804664010, ss2985282945, ss3022336596, ss3628883444, ss3634937137, ss3640644433, ss3644840492, ss3652819066, ss3654053320, ss3744521535, ss3745237382, ss3761282378, ss3772732194, ss3823993374, ss3904145325, ss5346358979, ss5634169462, ss5847998373, ss5962544924 NC_000004.11:1377723:G:A NC_000004.12:1383935:G:A (self)
25555320, 137847062, 9726799, 320721, 437480596, 559608780, ss2259806655, ss3726101795, ss3771099252, ss3953348798, ss4600103040, ss5257734679, ss5456689752, ss5538029385, ss5861807688 NC_000004.12:1383935:G:A NC_000004.12:1383935:G:A (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 rs139310992

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