Name: rs2532331
Published: September 21, 2022
License: Open Access

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.

rs2532331

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:46270960 (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=0.109998 (14582/132566, GnomAD)
A=0.16319 (6340/38850, ALFA)
A=0.00046 (13/28258, 14KJPN) (+ 11 more)
A=0.00036 (6/16760, 8.3KJPN)
A=0.0781 (500/6404, 1000G_30x)
A=0.0003 (1/2922, KOREAN)
A=0.213 (213/998, GoNL)
A=0.112 (67/600, NorthernSweden)
A=0.067 (22/328, HapMap)
A=0.162 (35/216, Qatari)
G=0.50 (39/78, SGDP_PRJ)
A=0.50 (39/78, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LRRC37A : 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	38850	G=0.83681	A=0.16319
European	Sub	31308	G=0.82640	A=0.17360
African	Sub	2816	G=0.9581	A=0.0419
African Others	Sub	108	G=0.991	A=0.009
African American	Sub	2708	G=0.9568	A=0.0432
Asian	Sub	108	G=1.000	A=0.000
East Asian	Sub	84	G=1.00	A=0.00
Other Asian	Sub	24	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.836	A=0.164
Latin American 2	Sub	610	G=0.882	A=0.118
South Asian	Sub	94	G=0.93	A=0.07
Other	Sub	3768	G=0.8185	A=0.1815

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	132566	G=0.890002	A=0.109998
gnomAD - Genomes	European	Sub	70290	G=0.85083	A=0.14917
gnomAD - Genomes	African	Sub	41370	G=0.96294	A=0.03706
gnomAD - Genomes	American	Sub	12734	G=0.86328	A=0.13672
gnomAD - Genomes	East Asian	Sub	3128	G=0.9990	A=0.0010
gnomAD - Genomes	Ashkenazi Jewish	Sub	3046	G=0.8145	A=0.1855
gnomAD - Genomes	Other	Sub	1998	G=0.8724	A=0.1276
Allele Frequency Aggregator	Total	Global	38850	G=0.83681	A=0.16319
Allele Frequency Aggregator	European	Sub	31308	G=0.82640	A=0.17360
Allele Frequency Aggregator	Other	Sub	3768	G=0.8185	A=0.1815
Allele Frequency Aggregator	African	Sub	2816	G=0.9581	A=0.0419
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.882	A=0.118
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.836	A=0.164
Allele Frequency Aggregator	Asian	Sub	108	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	94	G=0.93	A=0.07
14KJPN	JAPANESE	Study-wide	28258	G=0.99954	A=0.00046
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99964	A=0.00036
1000Genomes_30x	Global	Study-wide	6404	G=0.9219	A=0.0781
1000Genomes_30x	African	Sub	1786	G=0.9860	A=0.0140
1000Genomes_30x	Europe	Sub	1266	G=0.7891	A=0.2109
1000Genomes_30x	South Asian	Sub	1202	G=0.9393	A=0.0607
1000Genomes_30x	East Asian	Sub	1170	G=0.9991	A=0.0009
1000Genomes_30x	American	Sub	980	G=0.863	A=0.137
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9997	A=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.787	A=0.213
Northern Sweden	ACPOP	Study-wide	600	G=0.888	A=0.112
HapMap	Global	Study-wide	328	G=0.933	A=0.067
HapMap	African	Sub	120	G=1.000	A=0.000
HapMap	American	Sub	118	G=0.814	A=0.186
HapMap	Asian	Sub	90	G=1.00	A=0.00
Qatari	Global	Study-wide	216	G=0.838	A=0.162
SGDP_PRJ	Global	Study-wide	78	G=0.50	A=0.50
Siberian	Global	Study-wide	4	G=0.5	A=0.5

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 17	NC_000017.11:g.46270960G>A
GRCh37.p13 chr 17	NC_000017.10:g.44348326G>A
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.515665T>C
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.517658T>C
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.973348G>A

Gene: LRRC37A, leucine rich repeat containing 37A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC37A transcript	NM_014834.4:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X9	XM_047437205.1:c.101+2280… XM_047437205.1:c.101+22801G>A	N/A	Intron Variant
LRRC37A transcript variant X1	XM_047437196.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X2	XM_047437197.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X3	XM_047437198.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X4	XM_047437199.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X10	XM_047437200.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X5	XM_047437201.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X6	XM_047437202.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X11	XM_047437203.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X7	XM_047437204.1:c.	N/A	Genic Upstream Transcript Variant
LRRC37A transcript variant X8	XM_047437206.1:c.	N/A	Genic Upstream Transcript Variant

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

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 17	NC_000017.11:g.46270960=	NC_000017.11:g.46270960G>A
GRCh37.p13 chr 17	NC_000017.10:g.44348326=	NC_000017.10:g.44348326G>A
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.515665T>C	NT_167251.2:g.515665=
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.517658T>C	NT_167251.1:g.517658=
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.973348=	NT_187663.1:g.973348G>A
LRRC37A transcript variant X9	XM_005257886.1:c.101+22801=	XM_005257886.1:c.101+22801G>A
LRRC37A transcript variant X10	XM_005257887.1:c.26+22801=	XM_005257887.1:c.26+22801G>A
LRRC37A transcript variant X9	XM_047437205.1:c.101+22801=	XM_047437205.1:c.101+22801G>A

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#.

36 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3549956	Sep 28, 2001 (100)
2	BCMHGSC_JDW	ss90600009	Mar 24, 2008 (129)
3	ENSEMBL	ss137088831	Dec 01, 2009 (137)
4	COMPLETE_GENOMICS	ss171460319	Jul 04, 2010 (132)
5	BUSHMAN	ss202551081	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss207820366	Jul 04, 2010 (132)
7	1000GENOMES	ss237252611	Jul 15, 2010 (137)
8	SSMP	ss661092322	Apr 25, 2013 (138)
9	EVA-GONL	ss993133932	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1081075399	Aug 21, 2014 (142)
11	HAMMER_LAB	ss1808794668	Sep 08, 2015 (146)
12	WEILL_CORNELL_DGM	ss1936595316	Feb 12, 2016 (147)
13	JJLAB	ss2029074245	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2157547567	Dec 20, 2016 (150)
15	SWEGEN	ss3015580343	Nov 08, 2017 (151)
16	BIOINF_KMB_FNS_UNIBA	ss3028358642	Nov 08, 2017 (151)
17	EVA_DECODE	ss3700519694	Jul 13, 2019 (153)
18	ACPOP	ss3742048662	Jul 13, 2019 (153)
19	ILLUMINA	ss3744445370	Jul 13, 2019 (153)
20	EVA	ss3754698140	Jul 13, 2019 (153)
21	PACBIO	ss3788214378	Jul 13, 2019 (153)
22	PACBIO	ss3793170161	Jul 13, 2019 (153)
23	EVA	ss3834881516	Apr 27, 2020 (154)
24	EVA	ss3841051813	Apr 27, 2020 (154)
25	EVA	ss3846548948	Apr 27, 2020 (154)
26	SGDP_PRJ	ss3885803989	Apr 27, 2020 (154)
27	KRGDB	ss3935504606	Apr 27, 2020 (154)
28	TOMMO_GENOMICS	ss5222544910	Apr 27, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5303227226	Oct 16, 2022 (156)
30	EVA	ss5427758687	Oct 16, 2022 (156)
31	HUGCELL_USP	ss5496269307	Oct 16, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5606990486	Oct 16, 2022 (156)
33	SANFORD_IMAGENETICS	ss5660155011	Oct 16, 2022 (156)
34	TOMMO_GENOMICS	ss5778797478	Oct 16, 2022 (156)
35	EVA	ss5834020867	Oct 16, 2022 (156)
36	EVA	ss5951545741	Oct 16, 2022 (156)
37	1000Genomes_30x	NC_000017.11 - 46270960	Oct 16, 2022 (156)
38	gnomAD - Genomes	NC_000017.11 - 46270960	Apr 27, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000017.10 - 44348326	Apr 27, 2020 (154)
40	HapMap	NC_000017.11 - 46270960	Apr 27, 2020 (154)
41	KOREAN population from KRGDB	NC_000017.10 - 44348326	Apr 27, 2020 (154)
42	Northern Sweden	NC_000017.10 - 44348326	Jul 13, 2019 (153)
43	Qatari	NC_000017.10 - 44348326	Apr 27, 2020 (154)
44	SGDP_PRJ	NC_000017.10 - 44348326	Apr 27, 2020 (154)
45	Siberian	NC_000017.10 - 44348326	Apr 27, 2020 (154)
46	8.3KJPN	NC_000017.10 - 44348326	Apr 27, 2021 (155)
47	14KJPN	NC_000017.11 - 46270960	Oct 16, 2022 (156)
48	ALFA	NC_000017.11 - 46270960	Apr 27, 2021 (155)

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)
rs77631785	May 04, 2012 (137)
rs116899793	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss90600009, ss171460319, ss202551081, ss207820366	NC_000017.9:41704102:G:A	NC_000017.11:46270959:G:A	(self)
17784414, 42682000, 15333527, 18637238, 37820969, 10063921, 80514217, ss237252611, ss661092322, ss993133932, ss1081075399, ss1808794668, ss1936595316, ss2029074245, ss2157547567, ss3015580343, ss3742048662, ss3744445370, ss3754698140, ss3788214378, ss3793170161, ss3834881516, ss3841051813, ss3885803989, ss3935504606, ss5222544910, ss5427758687, ss5660155011, ss5834020867, ss5951545741	NC_000017.10:44348325:G:A	NC_000017.11:46270959:G:A	(self)
94516421, 508025022, 1492190, 112634582, 6104622919, ss3028358642, ss3700519694, ss3846548948, ss5303227226, ss5496269307, ss5606990486, ss5778797478	NC_000017.11:46270959:G:A	NC_000017.11:46270959:G:A	(self)
ss3549956, ss137088831	NT_010783.15:9622477:G:A	NC_000017.11:46270959:G:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs2532331

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2532331