Name: rs372067263
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.

rs372067263

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:158645223 (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=0.000098 (26/264690, TOPMED)
A=0.000072 (18/249292, GnomAD_exome)
A=0.000107 (15/140182, GnomAD) (+ 10 more)
A=0.000075 (9/120698, ExAC)
A=0.00007 (3/44416, ALFA)
A=0.00028 (8/28256, 14KJPN)
A=0.00036 (6/16760, 8.3KJPN)
A=0.00017 (2/12084, GO-ESP)
A=0.0005 (2/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.0011 (2/1832, Korea1K)
A=0.014 (3/216, Qatari)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SPTA1 : 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	60776	G=0.99992	A=0.00008
European	Sub	42736	G=0.99988	A=0.00012
African	Sub	8350	G=1.0000	A=0.0000
African Others	Sub	306	G=1.000	A=0.000
African American	Sub	8044	G=1.0000	A=0.0000
Asian	Sub	168	G=1.000	A=0.000
East Asian	Sub	112	G=1.000	A=0.000
Other Asian	Sub	56	G=1.00	A=0.00
Latin American 1	Sub	500	G=1.000	A=0.000
Latin American 2	Sub	628	G=1.000	A=0.000
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	8296	G=1.0000	A=0.0000

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
TopMed	Global	Study-wide	264690	G=0.999902	A=0.000098
gnomAD - Exomes	Global	Study-wide	249292	G=0.999928	A=0.000072
gnomAD - Exomes	European	Sub	134628	G=0.999933	A=0.000067
gnomAD - Exomes	Asian	Sub	48576	G=0.99990	A=0.00010
gnomAD - Exomes	American	Sub	34484	G=0.99988	A=0.00012
gnomAD - Exomes	African	Sub	15484	G=1.00000	A=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	10068	G=1.00000	A=0.00000
gnomAD - Exomes	Other	Sub	6052	G=1.0000	A=0.0000
gnomAD - Genomes	Global	Study-wide	140182	G=0.999893	A=0.000107
gnomAD - Genomes	European	Sub	75900	G=0.99984	A=0.00016
gnomAD - Genomes	African	Sub	42042	G=0.99995	A=0.00005
gnomAD - Genomes	American	Sub	13642	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3128	G=0.9997	A=0.0003
gnomAD - Genomes	Other	Sub	2150	G=1.0000	A=0.0000
ExAC	Global	Study-wide	120698	G=0.999925	A=0.000075
ExAC	Europe	Sub	73348	G=0.99995	A=0.00005
ExAC	Asian	Sub	25134	G=0.99988	A=0.00012
ExAC	American	Sub	11514	G=0.99983	A=0.00017
ExAC	African	Sub	9802	G=1.0000	A=0.0000
ExAC	Other	Sub	900	G=1.000	A=0.000
Allele Frequency Aggregator	Total	Global	44416	G=0.99993	A=0.00007
Allele Frequency Aggregator	European	Sub	32648	G=0.99991	A=0.00009
Allele Frequency Aggregator	Other	Sub	6862	G=1.0000	A=0.0000
Allele Frequency Aggregator	African	Sub	3512	G=1.0000	A=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
14KJPN	JAPANESE	Study-wide	28256	G=0.99972	A=0.00028
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99964	A=0.00036
GO Exome Sequencing Project	Global	Study-wide	12084	G=0.99983	A=0.00017
GO Exome Sequencing Project	European American	Sub	8262	G=0.9998	A=0.0002
GO Exome Sequencing Project	African American	Sub	3822	G=1.0000	A=0.0000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9995	A=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9995	A=0.0005
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9997	A=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9989	A=0.0011
Qatari	Global	Study-wide	216	G=0.986	A=0.014

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 1	NC_000001.11:g.158645223G>A
GRCh37.p13 chr 1	NC_000001.10:g.158615013G>A
SPTA1 RefSeqGene (LRG_1131)	NG_011474.1:g.46494C>T

Gene: SPTA1, spectrin alpha, erythrocytic 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SPTA1 transcript	NM_003126.4:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1	NP_003117.2:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X1	XM_011509916.3:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X1	XP_011508218.1:p.Arg1387C… XP_011508218.1:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X2	XM_011509917.4:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X2	XP_011508219.1:p.Arg1387C… XP_011508219.1:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X3	XM_047428883.1:c.3838C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X3	XP_047284839.1:p.Arg1280C… XP_047284839.1:p.Arg1280Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X4	XM_011509918.4:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X4	XP_011508220.1:p.Arg1387C… XP_011508220.1:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X6	XM_011509919.4:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X5	XP_011508221.1:p.Arg1387C… XP_011508221.1:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X7	XM_047428888.1:c.4159C>T	R [CGC] > C [TGC]	Coding Sequence Variant
spectrin alpha chain, erythrocytic 1 isoform X6	XP_047284844.1:p.Arg1387C… XP_047284844.1:p.Arg1387Cys	R (Arg) > C (Cys)	Missense Variant
SPTA1 transcript variant X5	XR_921911.4:n.4357C>T	N/A	Non Coding 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.

Allele: A (allele ID: 1302121 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001765801.1	not provided	Uncertain-Significance

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 1	NC_000001.11:g.158645223=	NC_000001.11:g.158645223G>A
GRCh37.p13 chr 1	NC_000001.10:g.158615013=	NC_000001.10:g.158615013G>A
SPTA1 RefSeqGene (LRG_1131)	NG_011474.1:g.46494=	NG_011474.1:g.46494C>T
SPTA1 transcript	NM_003126.4:c.4159=	NM_003126.4:c.4159C>T
SPTA1 transcript	NM_003126.3:c.4159=	NM_003126.3:c.4159C>T
SPTA1 transcript	NM_003126.2:c.4159=	NM_003126.2:c.4159C>T
SPTA1 transcript variant X2	XM_011509917.4:c.4159=	XM_011509917.4:c.4159C>T
SPTA1 transcript variant X2	XM_011509917.3:c.4159=	XM_011509917.3:c.4159C>T
SPTA1 transcript variant X2	XM_011509917.2:c.4159=	XM_011509917.2:c.4159C>T
SPTA1 transcript variant X2	XM_011509917.1:c.4159=	XM_011509917.1:c.4159C>T
SPTA1 transcript variant X4	XM_011509918.4:c.4159=	XM_011509918.4:c.4159C>T
SPTA1 transcript variant X3	XM_011509918.3:c.4159=	XM_011509918.3:c.4159C>T
SPTA1 transcript variant X3	XM_011509918.2:c.4159=	XM_011509918.2:c.4159C>T
SPTA1 transcript variant X3	XM_011509918.1:c.4159=	XM_011509918.1:c.4159C>T
SPTA1 transcript variant X5	XR_921911.4:n.4357=	XR_921911.4:n.4357C>T
SPTA1 transcript variant X4	XR_921911.3:n.4285=	XR_921911.3:n.4285C>T
SPTA1 transcript variant X4	XR_921911.2:n.4273=	XR_921911.2:n.4273C>T
SPTA1 transcript variant X4	XR_921911.1:n.4272=	XR_921911.1:n.4272C>T
SPTA1 transcript variant X6	XM_011509919.4:c.4159=	XM_011509919.4:c.4159C>T
SPTA1 transcript variant X5	XM_011509919.3:c.4159=	XM_011509919.3:c.4159C>T
SPTA1 transcript variant X5	XM_011509919.2:c.4159=	XM_011509919.2:c.4159C>T
SPTA1 transcript variant X5	XM_011509919.1:c.4159=	XM_011509919.1:c.4159C>T
SPTA1 transcript variant X1	XM_011509916.3:c.4159=	XM_011509916.3:c.4159C>T
SPTA1 transcript variant X1	XM_011509916.2:c.4159=	XM_011509916.2:c.4159C>T
SPTA1 transcript variant X1	XM_011509916.1:c.4159=	XM_011509916.1:c.4159C>T
SPTA1 transcript variant X3	XM_047428883.1:c.3838=	XM_047428883.1:c.3838C>T
SPTA1 transcript variant X7	XM_047428888.1:c.4159=	XM_047428888.1:c.4159C>T
spectrin alpha chain, erythrocytic 1	NP_003117.2:p.Arg1387=	NP_003117.2:p.Arg1387Cys
spectrin alpha chain, erythrocytic 1 isoform X2	XP_011508219.1:p.Arg1387=	XP_011508219.1:p.Arg1387Cys
spectrin alpha chain, erythrocytic 1 isoform X4	XP_011508220.1:p.Arg1387=	XP_011508220.1:p.Arg1387Cys
spectrin alpha chain, erythrocytic 1 isoform X5	XP_011508221.1:p.Arg1387=	XP_011508221.1:p.Arg1387Cys
spectrin alpha chain, erythrocytic 1 isoform X1	XP_011508218.1:p.Arg1387=	XP_011508218.1:p.Arg1387Cys
spectrin alpha chain, erythrocytic 1 isoform X3	XP_047284839.1:p.Arg1280=	XP_047284839.1:p.Arg1280Cys
spectrin alpha chain, erythrocytic 1 isoform X6	XP_047284844.1:p.Arg1387=	XP_047284844.1:p.Arg1387Cys

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#.

16 SubSNP, 13 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss712343111	Apr 25, 2013 (138)
2	EVA_UK10K_ALSPAC	ss1601272116	Apr 01, 2015 (144)
3	EVA_UK10K_TWINSUK	ss1644266149	Apr 01, 2015 (144)
4	EVA_EXAC	ss1685855131	Apr 01, 2015 (144)
5	WEILL_CORNELL_DGM	ss1918945923	Feb 12, 2016 (147)
6	HUMAN_LONGEVITY	ss2166766640	Dec 20, 2016 (150)
7	GNOMAD	ss2731969304	Nov 08, 2017 (151)
8	GNOMAD	ss2746472549	Nov 08, 2017 (151)
9	GNOMAD	ss2761641548	Nov 08, 2017 (151)
10	EVA	ss3823673300	Apr 25, 2020 (154)
11	KRGDB	ss3895281276	Apr 25, 2020 (154)
12	KOGIC	ss3945711355	Apr 25, 2020 (154)
13	TOPMED	ss4469309487	Apr 25, 2021 (155)
14	TOMMO_GENOMICS	ss5146615030	Apr 25, 2021 (155)
15	TOMMO_GENOMICS	ss5673852765	Oct 12, 2022 (156)
16	EVA	ss5938441367	Oct 12, 2022 (156)
17	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 158615013	Oct 11, 2018 (152)
18	ExAC	NC_000001.10 - 158615013	Oct 11, 2018 (152)
19	gnomAD - Genomes	NC_000001.11 - 158645223	Apr 25, 2021 (155)
20	gnomAD - Exomes	NC_000001.10 - 158615013	Jul 12, 2019 (153)
21	GO Exome Sequencing Project	NC_000001.10 - 158615013	Oct 11, 2018 (152)
22	KOREAN population from KRGDB	NC_000001.10 - 158615013	Apr 25, 2020 (154)
23	Korean Genome Project	NC_000001.11 - 158645223	Apr 25, 2020 (154)
24	Qatari	NC_000001.10 - 158615013	Apr 25, 2020 (154)
25	8.3KJPN	NC_000001.10 - 158615013	Apr 25, 2021 (155)
26	14KJPN	NC_000001.11 - 158645223	Oct 12, 2022 (156)
27	TopMed	NC_000001.11 - 158645223	Apr 25, 2021 (155)
28	UK 10K study - Twins	NC_000001.10 - 158615013	Oct 11, 2018 (152)
29	ALFA	NC_000001.11 - 158645223	Apr 25, 2021 (155)
30	ClinVar	RCV001765801.1	Oct 12, 2022 (156)

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
2084978, 5077112, 994320, 131879, 2458670, 987853, 4584337, 2084978, ss712343111, ss1601272116, ss1644266149, ss1685855131, ss1918945923, ss2731969304, ss2746472549, ss2761641548, ss3823673300, ss3895281276, ss5146615030, ss5938441367	NC_000001.10:158615012:G:A	NC_000001.11:158645222:G:A	(self)
RCV001765801.1, 27883613, 2089356, 7689869, 32915822, 3129872881, ss2166766640, ss3945711355, ss4469309487, ss5673852765	NC_000001.11:158645222:G:A	NC_000001.11:158645222: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 rs372067263

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

rs372067263