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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.

rs114136713

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:43211512 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.002660 (704/264690, TOPMED)
G=0.001333 (335/251404, GnomAD_exome)
G=0.002053 (288/140270, GnomAD) (+ 11 more)
G=0.001236 (150/121362, ExAC)
G=0.00114 (56/49294, ALFA)
G=0.00223 (29/13004, GO-ESP)
G=0.0031 (20/6404, 1000G_30x)
G=0.0028 (14/5008, 1000G)
G=0.0004 (2/4480, Estonian)
G=0.0008 (3/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.005 (1/216, Qatari)
A=0.5 (3/6, SGDP_PRJ)
G=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
EPB42 : Synonymous 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 65634 A=0.99869 G=0.00131
European Sub 47338 A=0.99920 G=0.00080
African Sub 8412 A=0.9966 G=0.0034
African Others Sub 306 A=1.000 G=0.000
African American Sub 8106 A=0.9964 G=0.0036
Asian Sub 168 A=1.000 G=0.000
East Asian Sub 112 A=1.000 G=0.000
Other Asian Sub 56 A=1.00 G=0.00
Latin American 1 Sub 500 A=0.996 G=0.004
Latin American 2 Sub 628 A=0.995 G=0.005
South Asian Sub 98 A=1.00 G=0.00
Other Sub 8490 A=0.9984 G=0.0016


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 A=0.997340 G=0.002660
gnomAD - Exomes Global Study-wide 251404 A=0.998667 G=0.001333
gnomAD - Exomes European Sub 135336 A=0.999232 G=0.000768
gnomAD - Exomes Asian Sub 49010 A=0.99990 G=0.00010
gnomAD - Exomes American Sub 34590 A=0.99734 G=0.00266
gnomAD - Exomes African Sub 16254 A=0.99483 G=0.00517
gnomAD - Exomes Ashkenazi Jewish Sub 10076 A=0.99712 G=0.00288
gnomAD - Exomes Other Sub 6138 A=0.9966 G=0.0034
gnomAD - Genomes Global Study-wide 140270 A=0.997947 G=0.002053
gnomAD - Genomes European Sub 75954 A=0.99959 G=0.00041
gnomAD - Genomes African Sub 42044 A=0.99512 G=0.00488
gnomAD - Genomes American Sub 13664 A=0.99707 G=0.00293
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9982 G=0.0018
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9972 G=0.0028
ExAC Global Study-wide 121362 A=0.998764 G=0.001236
ExAC Europe Sub 73324 A=0.99921 G=0.00079
ExAC Asian Sub 25164 A=0.99996 G=0.00004
ExAC American Sub 11576 A=0.99698 G=0.00302
ExAC African Sub 10390 A=0.99461 G=0.00539
ExAC Other Sub 908 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 49294 A=0.99886 G=0.00114
Allele Frequency Aggregator European Sub 37270 A=0.99922 G=0.00078
Allele Frequency Aggregator Other Sub 7056 A=0.9984 G=0.0016
Allele Frequency Aggregator African Sub 3574 A=0.9969 G=0.0031
Allele Frequency Aggregator Latin American 2 Sub 628 A=0.995 G=0.005
Allele Frequency Aggregator Latin American 1 Sub 500 A=0.996 G=0.004
Allele Frequency Aggregator Asian Sub 168 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13004 A=0.99777 G=0.00223
GO Exome Sequencing Project European American Sub 8598 A=0.9987 G=0.0013
GO Exome Sequencing Project African American Sub 4406 A=0.9959 G=0.0041
1000Genomes_30x Global Study-wide 6404 A=0.9969 G=0.0031
1000Genomes_30x African Sub 1786 A=0.9922 G=0.0078
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.994 G=0.006
1000Genomes Global Study-wide 5008 A=0.9972 G=0.0028
1000Genomes African Sub 1322 A=0.9924 G=0.0076
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.994 G=0.006
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9996 G=0.0004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9992 G=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 G=0.0000
Qatari Global Study-wide 216 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 6 A=0.5 G=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 15 NC_000015.10:g.43211512A>G
GRCh37.p13 chr 15 NC_000015.9:g.43503710A>G
EPB42 RefSeqGene (LRG_1171) NG_011505.2:g.19345T>C
Gene: EPB42, erythrocyte membrane protein band 4.2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPB42 transcript variant 1 NM_000119.3:c.543T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform 1 NP_000110.2:p.Asn181= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant 2 NM_001114134.2:c.453T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform 2 NP_001107606.1:p.Asn151= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant X6 XM_011521354.2:c.-13= N/A 5 Prime UTR Variant
EPB42 transcript variant X1 XM_011521350.3:c.543T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform X1 XP_011519652.1:p.Asn181= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant X2 XM_011521351.3:c.543T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform X1 XP_011519653.1:p.Asn181= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant X3 XM_011521352.3:c.507T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform X2 XP_011519654.1:p.Asn169= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant X4 XM_011521353.3:c.543T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform X3 XP_011519655.1:p.Asn181= N (Asn) > N (Asn) Synonymous Variant
EPB42 transcript variant X5 XM_005254225.2:c.453T>C N [AAT] > N [AAC] Coding Sequence Variant
protein 4.2 isoform X4 XP_005254282.1:p.Asn151= N (Asn) > N (Asn) Synonymous 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: G (allele ID: 255223 )
ClinVar Accession Disease Names Clinical Significance
RCV000249878.1 not specified Likely-Benign
RCV000329505.6 Hereditary spherocytosis type 5 Conflicting-Interpretations-Of-Pathogenicity
RCV000889760.4 not provided 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 A= G
GRCh38.p14 chr 15 NC_000015.10:g.43211512= NC_000015.10:g.43211512A>G
GRCh37.p13 chr 15 NC_000015.9:g.43503710= NC_000015.9:g.43503710A>G
EPB42 RefSeqGene (LRG_1171) NG_011505.2:g.19345= NG_011505.2:g.19345T>C
EPB42 transcript variant 1 NM_000119.3:c.543= NM_000119.3:c.543T>C
EPB42 transcript variant 1 NM_000119.2:c.543= NM_000119.2:c.543T>C
EPB42 transcript variant 2 NM_001114134.2:c.453= NM_001114134.2:c.453T>C
EPB42 transcript variant 2 NM_001114134.1:c.453= NM_001114134.1:c.453T>C
EPB42 transcript variant X1 XM_011521350.3:c.543= XM_011521350.3:c.543T>C
EPB42 transcript variant X2 XM_011521350.2:c.543= XM_011521350.2:c.543T>C
EPB42 transcript variant X2 XM_011521350.1:c.543= XM_011521350.1:c.543T>C
EPB42 transcript variant X2 XM_011521351.3:c.543= XM_011521351.3:c.543T>C
EPB42 transcript variant X3 XM_011521351.2:c.543= XM_011521351.2:c.543T>C
EPB42 transcript variant X3 XM_011521351.1:c.543= XM_011521351.1:c.543T>C
EPB42 transcript variant X3 XM_011521352.3:c.507= XM_011521352.3:c.507T>C
EPB42 transcript variant X4 XM_011521352.2:c.507= XM_011521352.2:c.507T>C
EPB42 transcript variant X4 XM_011521352.1:c.507= XM_011521352.1:c.507T>C
EPB42 transcript variant X4 XM_011521353.3:c.543= XM_011521353.3:c.543T>C
EPB42 transcript variant X5 XM_011521353.2:c.543= XM_011521353.2:c.543T>C
EPB42 transcript variant X5 XM_011521353.1:c.543= XM_011521353.1:c.543T>C
EPB42 transcript variant X5 XM_005254225.2:c.453= XM_005254225.2:c.453T>C
EPB42 transcript variant X6 XM_005254225.1:c.453= XM_005254225.1:c.453T>C
EPB42 transcript variant X6 XM_011521354.2:c.-13= XM_011521354.2:c.-13T>C
EPB42 transcript variant X7 XM_011521354.1:c.-13= XM_011521354.1:c.-13T>C
protein 4.2 isoform 1 NP_000110.2:p.Asn181= NP_000110.2:p.Asn181=
protein 4.2 isoform 2 NP_001107606.1:p.Asn151= NP_001107606.1:p.Asn151=
protein 4.2 isoform X1 XP_011519652.1:p.Asn181= XP_011519652.1:p.Asn181=
protein 4.2 isoform X1 XP_011519653.1:p.Asn181= XP_011519653.1:p.Asn181=
protein 4.2 isoform X2 XP_011519654.1:p.Asn169= XP_011519654.1:p.Asn169=
protein 4.2 isoform X3 XP_011519655.1:p.Asn181= XP_011519655.1:p.Asn181=
protein 4.2 isoform X4 XP_005254282.1:p.Asn151= XP_005254282.1:p.Asn151=
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#.

29 SubSNP, 13 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217427596 Jul 14, 2010 (132)
2 1000GENOMES ss217429949 Jul 14, 2010 (132)
3 NHLBI-ESP ss342401636 May 09, 2011 (134)
4 1000GENOMES ss464133701 Sep 17, 2011 (135)
5 1000GENOMES ss491081541 May 04, 2012 (137)
6 1000GENOMES ss1353226907 Aug 21, 2014 (142)
7 EVA_UK10K_ALSPAC ss1632873361 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1675867394 Apr 01, 2015 (144)
9 EVA_EXAC ss1691793247 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1935131611 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2206302400 Dec 20, 2016 (150)
12 GNOMAD ss2741190121 Nov 08, 2017 (151)
13 GNOMAD ss2749288934 Nov 08, 2017 (151)
14 GNOMAD ss2934209402 Nov 08, 2017 (151)
15 EGCUT_WGS ss3680331701 Jul 13, 2019 (153)
16 EVA_DECODE ss3697779555 Jul 13, 2019 (153)
17 EVA ss3824912403 Apr 27, 2020 (154)
18 SGDP_PRJ ss3882793957 Apr 27, 2020 (154)
19 EVA ss3986645594 Apr 26, 2021 (155)
20 TOPMED ss4989246753 Apr 26, 2021 (155)
21 1000G_HIGH_COVERAGE ss5298234792 Oct 16, 2022 (156)
22 EVA ss5418856247 Oct 16, 2022 (156)
23 HUGCELL_USP ss5491987327 Oct 16, 2022 (156)
24 1000G_HIGH_COVERAGE ss5599530651 Oct 16, 2022 (156)
25 EVA ss5624052417 Oct 16, 2022 (156)
26 EVA ss5828124212 Oct 16, 2022 (156)
27 EVA ss5848400511 Oct 16, 2022 (156)
28 EVA ss5875640978 Oct 16, 2022 (156)
29 EVA ss5948790401 Oct 16, 2022 (156)
30 1000Genomes NC_000015.9 - 43503710 Oct 12, 2018 (152)
31 1000Genomes_30x NC_000015.10 - 43211512 Oct 16, 2022 (156)
32 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 43503710 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000015.9 - 43503710 Oct 12, 2018 (152)
34 ExAC NC_000015.9 - 43503710 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000015.10 - 43211512 Apr 26, 2021 (155)
36 gnomAD - Exomes NC_000015.9 - 43503710 Jul 13, 2019 (153)
37 GO Exome Sequencing Project NC_000015.9 - 43503710 Oct 12, 2018 (152)
38 Qatari NC_000015.9 - 43503710 Apr 27, 2020 (154)
39 SGDP_PRJ NC_000015.9 - 43503710 Apr 27, 2020 (154)
40 TopMed NC_000015.10 - 43211512 Apr 26, 2021 (155)
41 UK 10K study - Twins NC_000015.9 - 43503710 Oct 12, 2018 (152)
42 ALFA NC_000015.10 - 43211512 Apr 26, 2021 (155)
43 ClinVar RCV000249878.1 Oct 12, 2018 (152)
44 ClinVar RCV000329505.6 Oct 16, 2022 (156)
45 ClinVar RCV000889760.4 Oct 16, 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
ss217427596, ss217429949 NC_000015.8:41291001:A:G NC_000015.10:43211511:A:G (self)
66290168, 36799575, 26069949, 2164067, 10453749, 1369676, 17173541, 34810937, 36799575, ss342401636, ss464133701, ss491081541, ss1353226907, ss1632873361, ss1675867394, ss1691793247, ss1935131611, ss2741190121, ss2749288934, ss2934209402, ss3680331701, ss3824912403, ss3882793957, ss3986645594, ss5418856247, ss5624052417, ss5828124212, ss5848400511, ss5948790401 NC_000015.9:43503709:A:G NC_000015.10:43211511:A:G (self)
RCV000249878.1, RCV000329505.6, RCV000889760.4, 87056586, 467297134, 204792413, 13545416380, ss2206302400, ss3697779555, ss4989246753, ss5298234792, ss5491987327, ss5599530651, ss5875640978 NC_000015.10:43211511:A:G NC_000015.10:43211511:A:G (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 rs114136713
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.post761+d5e8e07