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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.

rs5751738

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:23803488 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.085179 (22546/264690, TOPMED)
G=0.075979 (10657/140262, GnomAD)
G=0.33455 (5607/16760, 8.3KJPN) (+ 13 more)
G=0.0801 (575/7182, ALFA)
G=0.1332 (667/5008, 1000G)
G=0.0670 (300/4480, Estonian)
G=0.0701 (270/3854, ALSPAC)
G=0.0618 (229/3708, TWINSUK)
G=0.3222 (944/2930, KOREAN)
G=0.060 (60/998, GoNL)
G=0.057 (34/600, NorthernSweden)
G=0.165 (88/534, MGP)
G=0.125 (65/520, SGDP_PRJ)
G=0.097 (21/216, Qatari)
G=0.264 (56/212, Vietnamese)
G=0.09 (5/56, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SMARCB1 : 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 22 NC_000022.11:g.23803488G>A
GRCh38.p13 chr 22 NC_000022.11:g.23803488G>C
GRCh38.p13 chr 22 NC_000022.11:g.23803488G>T
GRCh37.p13 chr 22 NC_000022.10:g.24145675G>A
GRCh37.p13 chr 22 NC_000022.10:g.24145675G>C
GRCh37.p13 chr 22 NC_000022.10:g.24145675G>T
SMARCB1 RefSeqGene (LRG_520) NG_009303.1:g.21526G>A
SMARCB1 RefSeqGene (LRG_520) NG_009303.1:g.21526G>C
SMARCB1 RefSeqGene (LRG_520) NG_009303.1:g.21526G>T
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG7 NT_187633.1:g.39850G>A
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG7 NT_187633.1:g.39850G>C
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG7 NT_187633.1:g.39850G>T
Gene: SMARCB1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SMARCB1 transcript variant 2 NM_001007468.3:c.601+66G>A N/A Intron Variant
SMARCB1 transcript variant 3 NM_001317946.2:c.655+66G>A N/A Intron Variant
SMARCB1 transcript variant 4 NM_001362877.2:c.682+66G>A N/A Intron Variant
SMARCB1 transcript variant 1 NM_003073.5:c.628+66G>A 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 7182 G=0.0801 A=0.0000, C=0.9199, T=0.0000
European Sub 6756 G=0.0749 A=0.0000, C=0.9251, T=0.0000
African Sub 160 G=0.138 A=0.000, C=0.863, T=0.000
African Others Sub 8 G=0.5 A=0.0, C=0.5, T=0.0
African American Sub 152 G=0.118 A=0.000, C=0.882, T=0.000
Asian Sub 6 G=0.3 A=0.0, C=0.7, T=0.0
East Asian Sub 4 G=0.5 A=0.0, C=0.5, T=0.0
Other Asian Sub 2 G=0.0 A=0.0, C=1.0, T=0.0
Latin American 1 Sub 0 G=0 A=0, C=0, T=0
Latin American 2 Sub 20 G=1.00 A=0.00, C=0.00, T=0.00
South Asian Sub 6 G=0.3 A=0.0, C=0.7, T=0.0
Other Sub 234 G=0.098 A=0.000, C=0.902, T=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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.085179 C=0.914821
gnomAD - Genomes Global Study-wide 140262 G=0.075979 C=0.924021
gnomAD - Genomes European Sub 75964 G=0.07134 C=0.92866
gnomAD - Genomes African Sub 42042 G=0.06527 C=0.93473
gnomAD - Genomes American Sub 13656 G=0.09058 C=0.90942
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.0689 C=0.9311
gnomAD - Genomes East Asian Sub 3122 G=0.2687 C=0.7313
gnomAD - Genomes Other Sub 2154 G=0.0877 C=0.9123
8.3KJPN JAPANESE Study-wide 16760 G=0.33455 C=0.66545
1000Genomes Global Study-wide 5008 G=0.1332 C=0.8668
1000Genomes African Sub 1322 G=0.0651 C=0.9349
1000Genomes East Asian Sub 1008 G=0.2649 C=0.7351
1000Genomes Europe Sub 1006 G=0.0567 C=0.9433
1000Genomes South Asian Sub 978 G=0.187 C=0.813
1000Genomes American Sub 694 G=0.107 C=0.893
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.0670 C=0.9330
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.0701 C=0.9299
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.0618 C=0.9382
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.3222 A=0.0000, C=0.6778
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.060 C=0.940
Northern Sweden ACPOP Study-wide 600 G=0.057 C=0.943
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.165 C=0.835
SGDP_PRJ Global Study-wide 520 G=0.125 C=0.875
Qatari Global Study-wide 216 G=0.097 C=0.903
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.264 C=0.736
Siberian Global Study-wide 56 G=0.09 C=0.91
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 C T
GRCh38.p13 chr 22 NC_000022.11:g.23803488= NC_000022.11:g.23803488G>A NC_000022.11:g.23803488G>C NC_000022.11:g.23803488G>T
GRCh37.p13 chr 22 NC_000022.10:g.24145675= NC_000022.10:g.24145675G>A NC_000022.10:g.24145675G>C NC_000022.10:g.24145675G>T
SMARCB1 RefSeqGene (LRG_520) NG_009303.1:g.21526= NG_009303.1:g.21526G>A NG_009303.1:g.21526G>C NG_009303.1:g.21526G>T
GRCh38.p13 chr 22 alt locus HSCHR22_1_CTG7 NT_187633.1:g.39850= NT_187633.1:g.39850G>A NT_187633.1:g.39850G>C NT_187633.1:g.39850G>T
SMARCB1 transcript variant 2 NM_001007468.1:c.601+66= NM_001007468.1:c.601+66G>A NM_001007468.1:c.601+66G>C NM_001007468.1:c.601+66G>T
SMARCB1 transcript variant 2 NM_001007468.3:c.601+66= NM_001007468.3:c.601+66G>A NM_001007468.3:c.601+66G>C NM_001007468.3:c.601+66G>T
SMARCB1 transcript variant 3 NM_001317946.2:c.655+66= NM_001317946.2:c.655+66G>A NM_001317946.2:c.655+66G>C NM_001317946.2:c.655+66G>T
SMARCB1 transcript variant 4 NM_001362877.2:c.682+66= NM_001362877.2:c.682+66G>A NM_001362877.2:c.682+66G>C NM_001362877.2:c.682+66G>T
SMARCB1 transcript variant 1 NM_003073.3:c.628+66= NM_003073.3:c.628+66G>A NM_003073.3:c.628+66G>C NM_003073.3:c.628+66G>T
SMARCB1 transcript variant 1 NM_003073.5:c.628+66= NM_003073.5:c.628+66G>A NM_003073.5:c.628+66G>C NM_003073.5:c.628+66G>T
SMARCB1 transcript variant X1 XM_005261718.1:c.655+66= XM_005261718.1:c.655+66G>A XM_005261718.1:c.655+66G>C XM_005261718.1:c.655+66G>T
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#.

75 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss7999784 Apr 21, 2003 (114)
2 BCM_SSAHASNP ss11011265 Jul 11, 2003 (117)
3 SC_SNP ss13388684 Dec 05, 2003 (119)
4 SSAHASNP ss21862923 Apr 05, 2004 (121)
5 EGP_SNPS ss48532394 Mar 13, 2006 (126)
6 KRIBB_YJKIM ss65828907 Nov 29, 2006 (127)
7 HGSV ss78621678 Dec 06, 2007 (129)
8 HGSV ss80460905 Dec 14, 2007 (130)
9 BCMHGSC_JDW ss91890190 Mar 24, 2008 (129)
10 BGI ss103846822 Dec 01, 2009 (131)
11 ILLUMINA-UK ss117372574 Feb 14, 2009 (130)
12 ENSEMBL ss138340141 Dec 01, 2009 (131)
13 ENSEMBL ss139733816 Dec 01, 2009 (131)
14 GMI ss157071616 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss167745600 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss168971550 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss171862527 Jul 04, 2010 (132)
18 BUSHMAN ss204059756 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss208829880 Jul 04, 2010 (132)
20 1000GENOMES ss212106725 Jul 14, 2010 (132)
21 1000GENOMES ss228632933 Jul 14, 2010 (132)
22 1000GENOMES ss238033323 Jul 15, 2010 (132)
23 1000GENOMES ss244160722 Jul 15, 2010 (132)
24 BL ss255858489 May 09, 2011 (134)
25 GMI ss283600816 May 04, 2012 (137)
26 GMI ss287554486 Apr 25, 2013 (138)
27 PJP ss292742409 May 09, 2011 (134)
28 TISHKOFF ss566579178 Apr 25, 2013 (138)
29 SSMP ss662507494 Apr 25, 2013 (138)
30 EVA-GONL ss995252860 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1082590099 Aug 21, 2014 (142)
32 1000GENOMES ss1366801774 Aug 21, 2014 (142)
33 DDI ss1429230373 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1639804893 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1682798926 Apr 01, 2015 (144)
36 EVA_DECODE ss1699321163 Apr 01, 2015 (144)
37 EVA_MGP ss1711563749 Apr 01, 2015 (144)
38 HAMMER_LAB ss1809747420 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1938819147 Feb 12, 2016 (147)
40 GENOMED ss1966658583 Feb 12, 2016 (147)
41 JJLAB ss2030181942 Sep 14, 2016 (149)
42 USC_VALOUEV ss2158794088 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2246620671 Dec 20, 2016 (150)
44 TOPMED ss2413518637 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2629589471 Nov 08, 2017 (151)
46 GRF ss2704542320 Nov 08, 2017 (151)
47 GNOMAD ss2973353670 Nov 08, 2017 (151)
48 SWEGEN ss3019150148 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3028928321 Nov 08, 2017 (151)
50 CSHL ss3352793543 Nov 08, 2017 (151)
51 TOPMED ss3374816971 Nov 08, 2017 (151)
52 TOPMED ss3374816972 Nov 08, 2017 (151)
53 OMUKHERJEE_ADBS ss3646564523 Oct 12, 2018 (152)
54 URBANLAB ss3651159464 Oct 12, 2018 (152)
55 EGCUT_WGS ss3685655349 Jul 13, 2019 (153)
56 EVA_DECODE ss3708011686 Jul 13, 2019 (153)
57 ACPOP ss3743850197 Jul 13, 2019 (153)
58 EVA ss3759267529 Jul 13, 2019 (153)
59 PACBIO ss3788802417 Jul 13, 2019 (153)
60 PACBIO ss3793672391 Jul 13, 2019 (153)
61 PACBIO ss3798558775 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3822434812 Jul 13, 2019 (153)
63 EVA ss3835942753 Apr 27, 2020 (154)
64 EVA ss3841599827 Apr 27, 2020 (154)
65 EVA ss3847114190 Apr 27, 2020 (154)
66 SGDP_PRJ ss3890347577 Apr 27, 2020 (154)
67 KRGDB ss3940738479 Apr 27, 2020 (154)
68 FSA-LAB ss3984231799 Apr 26, 2021 (155)
69 EVA ss3986856576 Apr 26, 2021 (155)
70 VINODS ss4034756435 Apr 26, 2021 (155)
71 TOPMED ss5106042885 Apr 26, 2021 (155)
72 TOMMO_GENOMICS ss5232199343 Apr 26, 2021 (155)
73 CPQ_GEN_INCA ss5236854562 Apr 26, 2021 (155)
74 CPQ_GEN_INCA ss5236859211 Apr 26, 2021 (155)
75 EVA ss5237255319 Apr 26, 2021 (155)
76 1000Genomes NC_000022.10 - 24145675 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 24145675 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000022.10 - 24145675 Oct 12, 2018 (152)
79 gnomAD - Genomes NC_000022.11 - 23803488 Apr 26, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000022.10 - 24145675 Apr 27, 2020 (154)
81 KOREAN population from KRGDB NC_000022.10 - 24145675 Apr 27, 2020 (154)
82 Medical Genome Project healthy controls from Spanish population NC_000022.10 - 24145675 Apr 27, 2020 (154)
83 Northern Sweden NC_000022.10 - 24145675 Jul 13, 2019 (153)
84 Qatari NC_000022.10 - 24145675 Apr 27, 2020 (154)
85 SGDP_PRJ NC_000022.10 - 24145675 Apr 27, 2020 (154)
86 Siberian NC_000022.10 - 24145675 Apr 27, 2020 (154)
87 8.3KJPN NC_000022.10 - 24145675 Apr 26, 2021 (155)
88 TopMed NC_000022.11 - 23803488 Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000022.10 - 24145675 Oct 12, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000022.10 - 24145675 Jul 13, 2019 (153)
91 ALFA NC_000022.11 - 23803488 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).

Associated ID History Updated (Build)
rs7292555 Aug 27, 2003 (117)
rs57587409 May 23, 2008 (130)
rs117289130 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
47915873, ss3940738479 NC_000022.10:24145674:G:A NC_000022.11:23803487:G:A (self)
4546353959 NC_000022.11:23803487:G:A NC_000022.11:23803487:G:A
ss78621678, ss80460905 NC_000022.8:22470228:G:C NC_000022.11:23803487:G:C (self)
ss91890190, ss117372574, ss167745600, ss168971550, ss171862527, ss204059756, ss208829880, ss212106725, ss255858489, ss283600816, ss287554486, ss292742409, ss1699321163 NC_000022.9:22475674:G:C NC_000022.11:23803487:G:C (self)
80340278, 44438619, 31393597, 19801380, 47915873, 679509, 17135062, 20861069, 42364557, 11310442, 90168650, 44438619, 9806083, ss228632933, ss238033323, ss244160722, ss566579178, ss662507494, ss995252860, ss1082590099, ss1366801774, ss1429230373, ss1639804893, ss1682798926, ss1711563749, ss1809747420, ss1938819147, ss1966658583, ss2030181942, ss2158794088, ss2413518637, ss2629589471, ss2704542320, ss2973353670, ss3019150148, ss3352793543, ss3646564523, ss3685655349, ss3743850197, ss3759267529, ss3788802417, ss3793672391, ss3798558775, ss3835942753, ss3841599827, ss3890347577, ss3940738479, ss3984231799, ss3986856576, ss5232199343, ss5236854562, ss5236859211 NC_000022.10:24145674:G:C NC_000022.11:23803487:G:C (self)
567356652, 238040671, 381151832, 4546353959, ss2246620671, ss3028928321, ss3374816971, ss3651159464, ss3708011686, ss3822434812, ss3847114190, ss5106042885, ss5237255319 NC_000022.11:23803487:G:C NC_000022.11:23803487:G:C (self)
ss11011265, ss13388684, ss21862923 NT_011520.9:3536243:G:C NC_000022.11:23803487:G:C (self)
ss7999784, ss48532394, ss65828907, ss103846822, ss138340141, ss139733816, ss157071616 NT_011520.12:3536243:G:C NC_000022.11:23803487:G:C (self)
ss4034756435 NT_187633.1:39849:G:C NC_000022.11:23803487:G:C
4546353959, ss3374816972 NC_000022.11:23803487:G:T NC_000022.11:23803487:G:T (self)
ss48532394 NT_011520.12:3536243:G:T NC_000022.11:23803487:G:T (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 rs5751738

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