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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.

rs35398738

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:167869666 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.002434 (612/251388, GnomAD_exome)
C=0.003033 (368/121342, ExAC)
C=0.01560 (1228/78698, PAGE_STUDY) (+ 7 more)
C=0.00129 (59/45790, ALFA)
C=0.01069 (139/13006, GO-ESP)
C=0.0114 (73/6404, 1000G_30x)
C=0.0116 (58/5008, 1000G)
C=0.005 (1/216, Qatari)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
B3GALT1 : Missense Variant
B3GALT1-AS1 : 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 62150 T=0.99646 C=0.00354, G=0.00000
European Sub 42998 T=0.99998 C=0.00002, G=0.00000
African Sub 8742 T=0.9772 C=0.0228, G=0.0000
African Others Sub 302 T=0.974 C=0.026, G=0.000
African American Sub 8440 T=0.9774 C=0.0226, G=0.0000
Asian Sub 206 T=1.000 C=0.000, G=0.000
East Asian Sub 148 T=1.000 C=0.000, G=0.000
Other Asian Sub 58 T=1.00 C=0.00, G=0.00
Latin American 1 Sub 508 T=0.992 C=0.008, G=0.000
Latin American 2 Sub 634 T=1.000 C=0.000, G=0.000
South Asian Sub 104 T=1.000 C=0.000, G=0.000
Other Sub 8958 T=0.9982 C=0.0018, G=0.0000


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
gnomAD - Exomes Global Study-wide 251388 T=0.997566 C=0.002434
gnomAD - Exomes European Sub 135366 T=0.999970 C=0.000030
gnomAD - Exomes Asian Sub 49002 T=0.99986 C=0.00014
gnomAD - Exomes American Sub 34558 T=0.99878 C=0.00122
gnomAD - Exomes African Sub 16254 T=0.96598 C=0.03402
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6130 T=0.9990 C=0.0010
ExAC Global Study-wide 121342 T=0.996967 C=0.003033
ExAC Europe Sub 73326 T=0.99997 C=0.00003
ExAC Asian Sub 25140 T=0.99992 C=0.00008
ExAC American Sub 11576 T=0.99888 C=0.00112
ExAC African Sub 10394 T=0.96633 C=0.03367
ExAC Other Sub 906 T=0.999 C=0.001
The PAGE Study Global Study-wide 78698 T=0.98440 C=0.01560
The PAGE Study AfricanAmerican Sub 32514 T=0.96780 C=0.03220
The PAGE Study Mexican Sub 10810 T=0.99944 C=0.00056
The PAGE Study Asian Sub 8318 T=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7916 T=0.9898 C=0.0102
The PAGE Study NativeHawaiian Sub 4534 T=0.9998 C=0.0002
The PAGE Study Cuban Sub 4230 T=0.9948 C=0.0052
The PAGE Study Dominican Sub 3828 T=0.9869 C=0.0131
The PAGE Study CentralAmerican Sub 2450 T=0.9951 C=0.0049
The PAGE Study SouthAmerican Sub 1982 T=0.9965 C=0.0035
The PAGE Study NativeAmerican Sub 1260 T=0.9984 C=0.0016
The PAGE Study SouthAsian Sub 856 T=1.000 C=0.000
Allele Frequency Aggregator Total Global 45790 T=0.99871 C=0.00129, G=0.00000
Allele Frequency Aggregator European Sub 32910 T=0.99997 C=0.00003, G=0.00000
Allele Frequency Aggregator Other Sub 7524 T=0.9987 C=0.0013, G=0.0000
Allele Frequency Aggregator African Sub 3904 T=0.9887 C=0.0113, G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 634 T=1.000 C=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 508 T=0.992 C=0.008, G=0.000
Allele Frequency Aggregator Asian Sub 206 T=1.000 C=0.000, G=0.000
Allele Frequency Aggregator South Asian Sub 104 T=1.000 C=0.000, G=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.98931 C=0.01069
GO Exome Sequencing Project European American Sub 8600 T=0.9999 C=0.0001
GO Exome Sequencing Project African American Sub 4406 T=0.9687 C=0.0313
1000Genomes_30x Global Study-wide 6404 T=0.9886 C=0.0114
1000Genomes_30x African Sub 1786 T=0.9630 C=0.0370
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.993 C=0.007
1000Genomes Global Study-wide 5008 T=0.9884 C=0.0116
1000Genomes African Sub 1322 T=0.9592 C=0.0408
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.994 C=0.006
Qatari Global Study-wide 216 T=0.995 C=0.005
SGDP_PRJ Global Study-wide 6 T=0.5 C=0.5
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.167869666T>C
GRCh38.p14 chr 2 NC_000002.12:g.167869666T>G
GRCh37.p13 chr 2 NC_000002.11:g.168726176T>C
GRCh37.p13 chr 2 NC_000002.11:g.168726176T>G
B3GALT1 RefSeqGene NG_050644.1:g.581606T>C
B3GALT1 RefSeqGene NG_050644.1:g.581606T>G
Gene: B3GALT1, beta-1,3-galactosyltransferase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
B3GALT1 transcript NM_020981.4:c.627T>C N [AAT] > N [AAC] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 NP_066191.1:p.Asn209= N (Asn) > N (Asn) Synonymous Variant
B3GALT1 transcript NM_020981.4:c.627T>G N [AAT] > K [AAG] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 NP_066191.1:p.Asn209Lys N (Asn) > K (Lys) Missense Variant
B3GALT1 transcript variant X1 XM_047446159.1:c.627T>C N [AAT] > N [AAC] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302115.1:p.Asn209= N (Asn) > N (Asn) Synonymous Variant
B3GALT1 transcript variant X1 XM_047446159.1:c.627T>G N [AAT] > K [AAG] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302115.1:p.Asn209Lys N (Asn) > K (Lys) Missense Variant
B3GALT1 transcript variant X2 XM_006712819.4:c.627T>C N [AAT] > N [AAC] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_006712882.1:p.Asn209= N (Asn) > N (Asn) Synonymous Variant
B3GALT1 transcript variant X2 XM_006712819.4:c.627T>G N [AAT] > K [AAG] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_006712882.1:p.Asn209Lys N (Asn) > K (Lys) Missense Variant
B3GALT1 transcript variant X3 XM_011512085.3:c.627T>C N [AAT] > N [AAC] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_011510387.1:p.Asn209= N (Asn) > N (Asn) Synonymous Variant
B3GALT1 transcript variant X3 XM_011512085.3:c.627T>G N [AAT] > K [AAG] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_011510387.1:p.Asn209Lys N (Asn) > K (Lys) Missense Variant
B3GALT1 transcript variant X4 XM_047446160.1:c.627T>C N [AAT] > N [AAC] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302116.1:p.Asn209= N (Asn) > N (Asn) Synonymous Variant
B3GALT1 transcript variant X4 XM_047446160.1:c.627T>G N [AAT] > K [AAG] Coding Sequence Variant
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302116.1:p.Asn209Lys N (Asn) > K (Lys) Missense Variant
Gene: B3GALT1-AS1, B3GALT1 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
B3GALT1-AS1 transcript NR_131227.1: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
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= C G
GRCh38.p14 chr 2 NC_000002.12:g.167869666= NC_000002.12:g.167869666T>C NC_000002.12:g.167869666T>G
GRCh37.p13 chr 2 NC_000002.11:g.168726176= NC_000002.11:g.168726176T>C NC_000002.11:g.168726176T>G
B3GALT1 RefSeqGene NG_050644.1:g.581606= NG_050644.1:g.581606T>C NG_050644.1:g.581606T>G
B3GALT1 transcript NM_020981.4:c.627= NM_020981.4:c.627T>C NM_020981.4:c.627T>G
B3GALT1 transcript NM_020981.3:c.627= NM_020981.3:c.627T>C NM_020981.3:c.627T>G
B3GALT1 transcript variant X2 XM_006712819.4:c.627= XM_006712819.4:c.627T>C XM_006712819.4:c.627T>G
B3GALT1 transcript variant X3 XM_006712819.3:c.627= XM_006712819.3:c.627T>C XM_006712819.3:c.627T>G
B3GALT1 transcript variant X3 XM_006712819.2:c.627= XM_006712819.2:c.627T>C XM_006712819.2:c.627T>G
B3GALT1 transcript variant X2 XM_006712819.1:c.627= XM_006712819.1:c.627T>C XM_006712819.1:c.627T>G
B3GALT1 transcript variant X3 XM_011512085.3:c.627= XM_011512085.3:c.627T>C XM_011512085.3:c.627T>G
B3GALT1 transcript variant X2 XM_011512085.2:c.627= XM_011512085.2:c.627T>C XM_011512085.2:c.627T>G
B3GALT1 transcript variant X4 XM_011512085.1:c.627= XM_011512085.1:c.627T>C XM_011512085.1:c.627T>G
B3GALT1 transcript variant X1 XM_047446159.1:c.627= XM_047446159.1:c.627T>C XM_047446159.1:c.627T>G
B3GALT1 transcript variant X4 XM_047446160.1:c.627= XM_047446160.1:c.627T>C XM_047446160.1:c.627T>G
beta-1,3-galactosyltransferase 1 NP_066191.1:p.Asn209= NP_066191.1:p.Asn209= NP_066191.1:p.Asn209Lys
beta-1,3-galactosyltransferase 1 isoform X1 XP_006712882.1:p.Asn209= XP_006712882.1:p.Asn209= XP_006712882.1:p.Asn209Lys
beta-1,3-galactosyltransferase 1 isoform X1 XP_011510387.1:p.Asn209= XP_011510387.1:p.Asn209= XP_011510387.1:p.Asn209Lys
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302115.1:p.Asn209= XP_047302115.1:p.Asn209= XP_047302115.1:p.Asn209Lys
beta-1,3-galactosyltransferase 1 isoform X1 XP_047302116.1:p.Asn209= XP_047302116.1:p.Asn209= XP_047302116.1:p.Asn209Lys
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#.

35 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48408614 Mar 14, 2006 (126)
2 SEATTLESEQ ss159703036 Dec 01, 2009 (131)
3 1000GENOMES ss330117932 May 09, 2011 (134)
4 NHLBI-ESP ss342084877 May 09, 2011 (134)
5 1000GENOMES ss489839312 May 04, 2012 (137)
6 CLINSEQ_SNP ss491794063 May 04, 2012 (137)
7 ILLUMINA ss533833143 Sep 08, 2015 (146)
8 JMKIDD_LAB ss1067442189 Aug 21, 2014 (142)
9 1000GENOMES ss1300328554 Aug 21, 2014 (142)
10 EVA_EXAC ss1686580785 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1920869551 Feb 12, 2016 (147)
12 ILLUMINA ss1958476578 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2236373156 Dec 20, 2016 (150)
14 GNOMAD ss2733088860 Nov 08, 2017 (151)
15 GNOMAD ss2746809133 Nov 08, 2017 (151)
16 GNOMAD ss2782537026 Nov 08, 2017 (151)
17 ILLUMINA ss3022037829 Nov 08, 2017 (151)
18 ILLUMINA ss3628215808 Oct 11, 2018 (152)
19 ILLUMINA ss3652482125 Oct 11, 2018 (152)
20 ILLUMINA ss3725843154 Jul 13, 2019 (153)
21 PAGE_CC ss3770963027 Jul 13, 2019 (153)
22 KHV_HUMAN_GENOMES ss3802048182 Jul 13, 2019 (153)
23 EVA ss3823823136 Apr 25, 2020 (154)
24 EVA ss3825612041 Apr 25, 2020 (154)
25 SGDP_PRJ ss3853922106 Apr 25, 2020 (154)
26 EVA ss3986202748 Apr 26, 2021 (155)
27 TOPMED ss4532889191 Apr 26, 2021 (155)
28 TOPMED ss4532889192 Apr 26, 2021 (155)
29 1000G_HIGH_COVERAGE ss5250881926 Oct 12, 2022 (156)
30 EVA ss5333941021 Oct 12, 2022 (156)
31 HUGCELL_USP ss5450608065 Oct 12, 2022 (156)
32 1000G_HIGH_COVERAGE ss5527626368 Oct 12, 2022 (156)
33 SANFORD_IMAGENETICS ss5630306158 Oct 12, 2022 (156)
34 EVA ss5933379044 Oct 12, 2022 (156)
35 EVA ss5956528050 Oct 12, 2022 (156)
36 1000Genomes NC_000002.11 - 168726176 Oct 11, 2018 (152)
37 1000Genomes_30x NC_000002.12 - 167869666 Oct 12, 2022 (156)
38 ExAC NC_000002.11 - 168726176 Oct 11, 2018 (152)
39 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 81151750 (NC_000002.12:167869665:T:C 1451/140246)
Row 81151751 (NC_000002.12:167869665:T:G 1/140250)

- Apr 26, 2021 (155)
40 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 81151750 (NC_000002.12:167869665:T:C 1451/140246)
Row 81151751 (NC_000002.12:167869665:T:G 1/140250)

- Apr 26, 2021 (155)
41 gnomAD - Exomes NC_000002.11 - 168726176 Jul 13, 2019 (153)
42 GO Exome Sequencing Project NC_000002.11 - 168726176 Oct 11, 2018 (152)
43 The PAGE Study NC_000002.12 - 167869666 Jul 13, 2019 (153)
44 Qatari NC_000002.11 - 168726176 Apr 25, 2020 (154)
45 SGDP_PRJ NC_000002.11 - 168726176 Apr 25, 2020 (154)
46 TopMed

Submission ignored due to conflicting rows:
Row 336712070 (NC_000002.12:167869665:T:C 2843/264690)
Row 336712071 (NC_000002.12:167869665:T:G 3/264690)

- Apr 26, 2021 (155)
47 TopMed

Submission ignored due to conflicting rows:
Row 336712070 (NC_000002.12:167869665:T:C 2843/264690)
Row 336712071 (NC_000002.12:167869665:T:G 3/264690)

- Apr 26, 2021 (155)
48 ALFA NC_000002.12 - 167869666 Apr 26, 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
ss491794063 NC_000002.10:168434421:T:C NC_000002.12:167869665:T:C (self)
11382148, 6472749, 2147834, 281567, 2911481, 5939086, ss330117932, ss342084877, ss489839312, ss533833143, ss1067442189, ss1300328554, ss1686580785, ss1920869551, ss1958476578, ss2733088860, ss2746809133, ss2782537026, ss3022037829, ss3628215808, ss3652482125, ss3823823136, ss3825612041, ss3853922106, ss3986202748, ss5333941021, ss5630306158, ss5956528050 NC_000002.11:168726175:T:C NC_000002.12:167869665:T:C (self)
15152303, 184496, 9604215530, ss2236373156, ss3725843154, ss3770963027, ss3802048182, ss4532889191, ss5250881926, ss5450608065, ss5527626368, ss5933379044 NC_000002.12:167869665:T:C NC_000002.12:167869665:T:C (self)
ss48408614, ss159703036 NT_005403.17:18935593:T:C NC_000002.12:167869665:T:C (self)
9604215530, ss4532889192 NC_000002.12:167869665:T:G NC_000002.12:167869665: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 rs35398738

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