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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.

rs56014374

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:99132622 (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=0.001273 (337/264690, TOPMED)
A=0.001031 (259/251094, GnomAD_exome)
A=0.001148 (161/140228, GnomAD) (+ 12 more)
A=0.001104 (134/121368, ExAC)
A=0.00642 (478/74492, ALFA)
A=0.00138 (18/13006, GO-ESP)
A=0.0003 (2/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
A=0.0027 (12/4480, Estonian)
A=0.0021 (8/3854, ALSPAC)
A=0.0027 (10/3708, TWINSUK)
A=0.001 (1/998, GoNL)
A=0.002 (1/534, MGP)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TGFBR1 : Missense Variant
Publications
1 citation
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 90930 G=0.99447 A=0.00553
European Sub 72070 G=0.99328 A=0.00672
African Sub 8398 G=0.9998 A=0.0002
African Others Sub 306 G=1.000 A=0.000
African American Sub 8092 G=0.9998 A=0.0002
Asian Sub 212 G=1.000 A=0.000
East Asian Sub 156 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 500 G=0.998 A=0.002
Latin American 2 Sub 648 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 9004 G=0.9982 A=0.0018


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=0.998727 A=0.001273
gnomAD - Exomes Global Study-wide 251094 G=0.998969 A=0.001031
gnomAD - Exomes European Sub 135060 G=0.998438 A=0.001562
gnomAD - Exomes Asian Sub 49010 G=0.99973 A=0.00027
gnomAD - Exomes American Sub 34570 G=0.99945 A=0.00055
gnomAD - Exomes African Sub 16256 G=0.99969 A=0.00031
gnomAD - Exomes Ashkenazi Jewish Sub 10070 G=0.99990 A=0.00010
gnomAD - Exomes Other Sub 6128 G=0.9984 A=0.0016
gnomAD - Genomes Global Study-wide 140228 G=0.998852 A=0.001148
gnomAD - Genomes European Sub 75940 G=0.99816 A=0.00184
gnomAD - Genomes African Sub 42030 G=0.99964 A=0.00036
gnomAD - Genomes American Sub 13648 G=0.99963 A=0.00037
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9997 A=0.0003
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
ExAC Global Study-wide 121368 G=0.998896 A=0.001104
ExAC Europe Sub 73336 G=0.99839 A=0.00161
ExAC Asian Sub 25166 G=0.99976 A=0.00024
ExAC American Sub 11552 G=0.99939 A=0.00061
ExAC African Sub 10406 G=0.99971 A=0.00029
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 74492 G=0.99358 A=0.00642
Allele Frequency Aggregator European Sub 61920 G=0.99254 A=0.00746
Allele Frequency Aggregator Other Sub 7554 G=0.9983 A=0.0017
Allele Frequency Aggregator African Sub 3560 G=0.9994 A=0.0006
Allele Frequency Aggregator Latin American 2 Sub 648 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=0.998 A=0.002
Allele Frequency Aggregator Asian Sub 212 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.99862 A=0.00138
GO Exome Sequencing Project European American Sub 8600 G=0.9981 A=0.0019
GO Exome Sequencing Project African American Sub 4406 G=0.9995 A=0.0005
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 A=0.0016
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=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9973 A=0.0027
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9979 A=0.0021
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9973 A=0.0027
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.999 A=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
SGDP_PRJ Global Study-wide 2 G=0.5 A=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 9 NC_000009.12:g.99132622G>A
GRCh37.p13 chr 9 NC_000009.11:g.101894904G>A
TGFBR1 RefSeqGene NG_007461.1:g.32493G>A
Gene: TGFBR1, transforming growth factor beta receptor 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TGFBR1 transcript variant 2 NM_001130916.3:c.343+3522…

NM_001130916.3:c.343+3522G>A

 		N/A Intron Variant
TGFBR1 transcript variant 1 NM_004612.4:c.457G>A V [GTC] > I [ATC] Coding Sequence Variant
TGF-beta receptor type-1 isoform 1 precursor NP_004603.1:p.Val153Ile V (Val) > I (Ile) Missense Variant
TGFBR1 transcript variant 3 NM_001306210.2:c.469G>A V [GTC] > I [ATC] Coding Sequence Variant
TGF-beta receptor type-1 isoform 3 precursor NP_001293139.1:p.Val157Ile V (Val) > I (Ile) Missense Variant
TGFBR1 transcript variant X1 XM_011518948.3:c.262G>A V [GTC] > I [ATC] Coding Sequence Variant
TGF-beta receptor type-1 isoform X1 XP_011517250.1:p.Val88Ile V (Val) > I (Ile) Missense Variant
TGFBR1 transcript variant X2 XM_011518949.3:c.250G>A V [GTC] > I [ATC] Coding Sequence Variant
TGF-beta receptor type-1 isoform X2 XP_011517251.1:p.Val84Ile V (Val) > I (Ile) Missense 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.

Allele: A (allele ID: 210162 )
ClinVar Accession Disease Names Clinical Significance
RCV000200131.4 not specified Likely-Benign
RCV000251582.15 Familial thoracic aortic aneurysm and aortic dissection Benign-Likely-Benign
RCV000292925.3 Loeys-Dietz syndrome Likely-Benign
RCV000349783.4 Loeys-Dietz syndrome 1 Likely-Benign
RCV000617065.1 Cardiovascular phenotype Likely-Benign
RCV001580027.4 not provided Benign-Likely-Benign
RCV002277548.1 Ehlers-Danlos syndrome Benign
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 9 NC_000009.12:g.99132622= NC_000009.12:g.99132622G>A
GRCh37.p13 chr 9 NC_000009.11:g.101894904= NC_000009.11:g.101894904G>A
TGFBR1 RefSeqGene NG_007461.1:g.32493= NG_007461.1:g.32493G>A
TGFBR1 transcript variant 1 NM_004612.4:c.457= NM_004612.4:c.457G>A
TGFBR1 transcript variant 1 NM_004612.3:c.457= NM_004612.3:c.457G>A
TGFBR1 transcript variant 1 NM_004612.2:c.457= NM_004612.2:c.457G>A
TGFBR1 transcript variant 3 NM_001306210.2:c.469= NM_001306210.2:c.469G>A
TGFBR1 transcript variant 3 NM_001306210.1:c.469= NM_001306210.1:c.469G>A
TGFBR1 transcript variant 8 NM_001407420.1:c.262= NM_001407420.1:c.262G>A
TGFBR1 transcript variant 16 NM_001407429.1:c.250= NM_001407429.1:c.250G>A
TGFBR1 transcript variant 9 NM_001407422.1:c.262= NM_001407422.1:c.262G>A
TGFBR1 transcript variant 26 NR_176361.1:n.550= NR_176361.1:n.550G>A
TGFBR1 transcript variant 13 NM_001407426.1:c.250= NM_001407426.1:c.250G>A
TGFBR1 transcript variant 15 NM_001407428.1:c.250= NM_001407428.1:c.250G>A
TGFBR1 transcript variant 14 NM_001407427.1:c.250= NM_001407427.1:c.250G>A
TGFBR1 transcript variant 25 NR_176360.1:n.686= NR_176360.1:n.686G>A
TGFBR1 transcript variant 18 NM_001407432.1:c.250= NM_001407432.1:c.250G>A
TGFBR1 transcript variant 17 NM_001407430.1:c.250= NM_001407430.1:c.250G>A
TGFBR1 transcript variant 6 NM_001407418.1:c.262= NM_001407418.1:c.262G>A
TGFBR1 transcript variant 10 NM_001407423.1:c.250= NM_001407423.1:c.250G>A
TGFBR1 transcript variant 27 NR_176362.1:n.562= NR_176362.1:n.562G>A
TGFBR1 transcript variant 12 NM_001407425.1:c.250= NM_001407425.1:c.250G>A
TGFBR1 transcript variant 28 NR_176363.1:n.550= NR_176363.1:n.550G>A
TGFBR1 transcript variant 11 NM_001407424.1:c.250= NM_001407424.1:c.250G>A
TGFBR1 transcript variant 7 NM_001407419.1:c.262= NM_001407419.1:c.262G>A
TGFBR1 transcript variant 19 NM_001407433.1:c.250= NM_001407433.1:c.250G>A
TGFBR1 transcript variant 20 NM_001407434.1:c.250= NM_001407434.1:c.250G>A
TGFBR1 transcript variant 4 NM_001407416.1:c.469= NM_001407416.1:c.469G>A
TGFBR1 transcript variant 5 NM_001407417.1:c.457= NM_001407417.1:c.457G>A
TGFBR1 transcript variant 21 NM_001407435.1:c.457= NM_001407435.1:c.457G>A
TGFBR1 transcript variant 22 NM_001407436.1:c.211= NM_001407436.1:c.211G>A
TGFBR1 transcript variant X1 XM_011518948.3:c.262= XM_011518948.3:c.262G>A
TGFBR1 transcript variant X1 XM_011518948.2:c.262= XM_011518948.2:c.262G>A
TGFBR1 transcript variant X2 XM_011518948.1:c.262= XM_011518948.1:c.262G>A
TGFBR1 transcript variant X2 XM_011518949.3:c.250= XM_011518949.3:c.250G>A
TGF-beta receptor type-1 isoform 1 precursor NP_004603.1:p.Val153= NP_004603.1:p.Val153Ile
TGF-beta receptor type-1 isoform 3 precursor NP_001293139.1:p.Val157= NP_001293139.1:p.Val157Ile
TGF-beta receptor type-1 isoform X1 XP_011517250.1:p.Val88= XP_011517250.1:p.Val88Ile
TGF-beta receptor type-1 isoform X2 XP_011517251.1:p.Val84= XP_011517251.1:p.Val84Ile
TGFBR1 transcript variant 2 NM_001130916.1:c.343+3522= NM_001130916.1:c.343+3522G>A
TGFBR1 transcript variant 2 NM_001130916.3:c.343+3522= NM_001130916.3:c.343+3522G>A
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#.

53 SubSNP, 14 Frequency, 7 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CANCER-GENOME ss74801630 Dec 06, 2007 (129)
2 RSG_UW ss212965392 Jul 04, 2010 (132)
3 NHLBI-ESP ss342278554 May 09, 2011 (134)
4 1000GENOMES ss488910730 May 04, 2012 (137)
5 GSK-GENETICS ss491279619 May 04, 2012 (137)
6 EXOME_CHIP ss491425374 May 04, 2012 (137)
7 CLINSEQ_SNP ss491939833 May 04, 2012 (137)
8 ILLUMINA ss780878796 Sep 08, 2015 (146)
9 ILLUMINA ss783564373 Sep 08, 2015 (146)
10 EVA-GONL ss986794164 Aug 21, 2014 (142)
11 1000GENOMES ss1334761593 Aug 21, 2014 (142)
12 EVA_DECODE ss1596430177 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1623189086 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1666183119 Apr 01, 2015 (144)
15 EVA_EXAC ss1689578523 Apr 01, 2015 (144)
16 EVA_MGP ss1711231367 Apr 01, 2015 (144)
17 ILLUMINA ss1752749530 Sep 08, 2015 (146)
18 ILLUMINA ss1917838531 Feb 12, 2016 (147)
19 ILLUMINA ss1946263822 Feb 12, 2016 (147)
20 ILLUMINA ss1959200474 Feb 12, 2016 (147)
21 HUMAN_LONGEVITY ss2312988593 Dec 20, 2016 (150)
22 ILLUMINA ss2711167487 Nov 08, 2017 (151)
23 GNOMAD ss2737750807 Nov 08, 2017 (151)
24 GNOMAD ss2748231525 Nov 08, 2017 (151)
25 GNOMAD ss2881250748 Nov 08, 2017 (151)
26 AFFY ss2985467959 Nov 08, 2017 (151)
27 SWEGEN ss3005308662 Nov 08, 2017 (151)
28 ILLUMINA ss3022947760 Nov 08, 2017 (151)
29 ILLUMINA ss3630314555 Oct 12, 2018 (152)
30 ILLUMINA ss3635223743 Oct 12, 2018 (152)
31 ILLUMINA ss3640931034 Oct 12, 2018 (152)
32 ILLUMINA ss3644997157 Oct 12, 2018 (152)
33 ILLUMINA ss3653501262 Oct 12, 2018 (152)
34 ILLUMINA ss3654232782 Oct 12, 2018 (152)
35 EGCUT_WGS ss3672842981 Jul 13, 2019 (153)
36 EVA_DECODE ss3724409436 Jul 13, 2019 (153)
37 ILLUMINA ss3744591238 Jul 13, 2019 (153)
38 ILLUMINA ss3745523663 Jul 13, 2019 (153)
39 ILLUMINA ss3773015577 Jul 13, 2019 (153)
40 EVA ss3824448257 Apr 26, 2020 (154)
41 EVA ss3825758949 Apr 26, 2020 (154)
42 SGDP_PRJ ss3872709340 Apr 26, 2020 (154)
43 EVA ss3986454949 Apr 26, 2021 (155)
44 TOPMED ss4829538608 Apr 26, 2021 (155)
45 1000G_HIGH_COVERAGE ss5281573221 Oct 13, 2022 (156)
46 EVA ss5389139648 Oct 13, 2022 (156)
47 HUGCELL_USP ss5477498014 Oct 13, 2022 (156)
48 1000G_HIGH_COVERAGE ss5574326088 Oct 13, 2022 (156)
49 EVA ss5623892518 Oct 13, 2022 (156)
50 EVA ss5829508268 Oct 13, 2022 (156)
51 EVA ss5848212990 Oct 13, 2022 (156)
52 EVA ss5917324248 Oct 13, 2022 (156)
53 EVA ss5977112508 Oct 13, 2022 (156)
54 1000Genomes NC_000009.11 - 101894904 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000009.12 - 99132622 Oct 13, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 101894904 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000009.11 - 101894904 Oct 12, 2018 (152)
58 ExAC NC_000009.11 - 101894904 Oct 12, 2018 (152)
59 gnomAD - Genomes NC_000009.12 - 99132622 Apr 26, 2021 (155)
60 gnomAD - Exomes NC_000009.11 - 101894904 Jul 13, 2019 (153)
61 GO Exome Sequencing Project NC_000009.11 - 101894904 Oct 12, 2018 (152)
62 Genome of the Netherlands Release 5 NC_000009.11 - 101894904 Apr 26, 2020 (154)
63 Medical Genome Project healthy controls from Spanish population NC_000009.11 - 101894904 Apr 26, 2020 (154)
64 SGDP_PRJ NC_000009.11 - 101894904 Apr 26, 2020 (154)
65 TopMed NC_000009.12 - 99132622 Apr 26, 2021 (155)
66 UK 10K study - Twins NC_000009.11 - 101894904 Oct 12, 2018 (152)
67 ALFA NC_000009.12 - 99132622 Apr 26, 2021 (155)
68 ClinVar RCV000200131.4 Oct 13, 2022 (156)
69 ClinVar RCV000251582.15 Oct 13, 2022 (156)
70 ClinVar RCV000292925.3 Oct 13, 2022 (156)
71 ClinVar RCV000349783.4 Oct 13, 2022 (156)
72 ClinVar RCV000617065.1 Oct 12, 2018 (152)
73 ClinVar RCV001580027.4 Oct 13, 2022 (156)
74 ClinVar RCV002277548.1 Oct 13, 2022 (156)
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
ss491279619, ss491939833, ss1596430177 NC_000009.10:100934724:G:A NC_000009.12:99132621:G:A (self)
47054384, 26137885, 18581229, 9708961, 6935682, 906031, 11664277, 347127, 24726320, 26137885, ss342278554, ss488910730, ss491425374, ss780878796, ss783564373, ss986794164, ss1334761593, ss1623189086, ss1666183119, ss1689578523, ss1711231367, ss1752749530, ss1917838531, ss1946263822, ss1959200474, ss2711167487, ss2737750807, ss2748231525, ss2881250748, ss2985467959, ss3005308662, ss3022947760, ss3630314555, ss3635223743, ss3640931034, ss3644997157, ss3653501262, ss3654232782, ss3672842981, ss3744591238, ss3745523663, ss3773015577, ss3824448257, ss3825758949, ss3872709340, ss3986454949, ss5389139648, ss5623892518, ss5829508268, ss5848212990, ss5977112508 NC_000009.11:101894903:G:A NC_000009.12:99132621:G:A (self)
RCV000200131.4, RCV000251582.15, RCV000292925.3, RCV000349783.4, RCV000617065.1, RCV001580027.4, RCV002277548.1, 61852023, 332647580, 666916169, 7701699303, ss2312988593, ss3724409436, ss4829538608, ss5281573221, ss5477498014, ss5574326088, ss5917324248 NC_000009.12:99132621:G:A NC_000009.12:99132621:G:A (self)
ss74801630, ss212965392 NT_008470.19:31059435:G:A NC_000009.12:99132621: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.

1 citation for rs56014374
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post774+babeb33