Name: rs749983780
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.

rs749983780

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:27364560 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000033 (4/121382, ExAC)
G=0.00000 (0/14050, ALFA)
T=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EIF2B4 : Missense Variant
GTF3C2-AS2 : 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	14050	A=1.00000	G=0.00000, T=0.00000
European	Sub	9690	A=1.0000	G=0.0000, T=0.0000
African	Sub	2898	A=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	A=1.000	G=0.000, T=0.000
African American	Sub	2784	A=1.0000	G=0.0000, T=0.0000
Asian	Sub	112	A=1.000	G=0.000, T=0.000
East Asian	Sub	86	A=1.00	G=0.00, T=0.00
Other Asian	Sub	26	A=1.00	G=0.00, T=0.00
Latin American 1	Sub	146	A=1.000	G=0.000, T=0.000
Latin American 2	Sub	610	A=1.000	G=0.000, T=0.000
South Asian	Sub	98	A=1.00	G=0.00, T=0.00
Other	Sub	496	A=1.000	G=0.000, T=0.000

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
ExAC	Global	Study-wide	121382	A=0.999967	T=0.000033
ExAC	Europe	Sub	73336	A=0.99996	T=0.00004
ExAC	Asian	Sub	25162	A=1.00000	T=0.00000
ExAC	American	Sub	11578	A=0.99991	T=0.00009
ExAC	African	Sub	10398	A=1.00000	T=0.00000
ExAC	Other	Sub	908	A=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	14050	A=1.00000	G=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	9690	A=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	2898	A=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	496	A=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	G=0.00, T=0.00

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 2	NC_000002.12:g.27364560A>G
GRCh38.p14 chr 2	NC_000002.12:g.27364560A>T
GRCh37.p13 chr 2	NC_000002.11:g.27587427A>G
GRCh37.p13 chr 2	NC_000002.11:g.27587427A>T
EIF2B4 RefSeqGene	NG_009305.1:g.10898T>C
EIF2B4 RefSeqGene	NG_009305.1:g.10898T>A

Gene: EIF2B4, eukaryotic translation initiation factor 2B subunit delta (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EIF2B4 transcript variant 2	NM_001034116.2:c.1412T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 2	NP_001029288.1:p.Val471Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 2	NM_001034116.2:c.1412T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 2	NP_001029288.1:p.Val471Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 3	NM_015636.4:c.1409T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 3	NP_056451.3:p.Val470Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 3	NM_015636.4:c.1409T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 3	NP_056451.3:p.Val470Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 1	NM_172195.4:c.1472T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 1	NP_751945.2:p.Val491Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 1	NM_172195.4:c.1472T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 1	NP_751945.2:p.Val491Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 4	NM_001318965.2:c.1475T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 4	NP_001305894.1:p.Val492Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 4	NM_001318965.2:c.1475T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 4	NP_001305894.1:p.Val492Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 7	NM_001318968.2:c.827T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 7	NP_001305897.1:p.Val276Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 7	NM_001318968.2:c.827T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 7	NP_001305897.1:p.Val276Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 5	NM_001318966.2:c.1367T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 5	NP_001305895.1:p.Val456Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 5	NM_001318966.2:c.1367T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 5	NP_001305895.1:p.Val456Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 8	NM_001318969.2:c.794T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 8	NP_001305898.1:p.Val265Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 8	NM_001318969.2:c.794T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 8	NP_001305898.1:p.Val265Asp	V (Val) > D (Asp)	Missense Variant
EIF2B4 transcript variant 6	NM_001318967.2:c.1319T>C	V [GTT] > A [GCT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 6	NP_001305896.1:p.Val440Ala	V (Val) > A (Ala)	Missense Variant
EIF2B4 transcript variant 6	NM_001318967.2:c.1319T>A	V [GTT] > D [GAT]	Coding Sequence Variant
translation initiation factor eIF2B subunit delta isoform 6	NP_001305896.1:p.Val440Asp	V (Val) > D (Asp)	Missense Variant

Gene: GTF3C2-AS2, uncharacterized GTF3C2-AS2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GTF3C2-AS2 transcript	XR_007086253.1:n.	N/A	Intron 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	A=	G	T
GRCh38.p14 chr 2	NC_000002.12:g.27364560=	NC_000002.12:g.27364560A>G	NC_000002.12:g.27364560A>T
GRCh37.p13 chr 2	NC_000002.11:g.27587427=	NC_000002.11:g.27587427A>G	NC_000002.11:g.27587427A>T
EIF2B4 RefSeqGene	NG_009305.1:g.10898=	NG_009305.1:g.10898T>C	NG_009305.1:g.10898T>A
EIF2B4 transcript variant 1	NM_172195.4:c.1472=	NM_172195.4:c.1472T>C	NM_172195.4:c.1472T>A
EIF2B4 transcript variant 1	NM_172195.3:c.1472=	NM_172195.3:c.1472T>C	NM_172195.3:c.1472T>A
EIF2B4 transcript variant 3	NM_015636.4:c.1409=	NM_015636.4:c.1409T>C	NM_015636.4:c.1409T>A
EIF2B4 transcript variant 3	NM_015636.3:c.1409=	NM_015636.3:c.1409T>C	NM_015636.3:c.1409T>A
EIF2B4 transcript variant 5	NM_001318966.2:c.1367=	NM_001318966.2:c.1367T>C	NM_001318966.2:c.1367T>A
EIF2B4 transcript variant 5	NM_001318966.1:c.1367=	NM_001318966.1:c.1367T>C	NM_001318966.1:c.1367T>A
EIF2B4 transcript variant 4	NM_001318965.2:c.1475=	NM_001318965.2:c.1475T>C	NM_001318965.2:c.1475T>A
EIF2B4 transcript variant 4	NM_001318965.1:c.1475=	NM_001318965.1:c.1475T>C	NM_001318965.1:c.1475T>A
EIF2B4 transcript variant 2	NM_001034116.2:c.1412=	NM_001034116.2:c.1412T>C	NM_001034116.2:c.1412T>A
EIF2B4 transcript variant 2	NM_001034116.1:c.1412=	NM_001034116.1:c.1412T>C	NM_001034116.1:c.1412T>A
EIF2B4 transcript variant 6	NM_001318967.2:c.1319=	NM_001318967.2:c.1319T>C	NM_001318967.2:c.1319T>A
EIF2B4 transcript variant 6	NM_001318967.1:c.1319=	NM_001318967.1:c.1319T>C	NM_001318967.1:c.1319T>A
EIF2B4 transcript variant 7	NM_001318968.2:c.827=	NM_001318968.2:c.827T>C	NM_001318968.2:c.827T>A
EIF2B4 transcript variant 7	NM_001318968.1:c.827=	NM_001318968.1:c.827T>C	NM_001318968.1:c.827T>A
EIF2B4 transcript variant 8	NM_001318969.2:c.794=	NM_001318969.2:c.794T>C	NM_001318969.2:c.794T>A
EIF2B4 transcript variant 8	NM_001318969.1:c.794=	NM_001318969.1:c.794T>C	NM_001318969.1:c.794T>A
translation initiation factor eIF2B subunit delta isoform 1	NP_751945.2:p.Val491=	NP_751945.2:p.Val491Ala	NP_751945.2:p.Val491Asp
translation initiation factor eIF2B subunit delta isoform 3	NP_056451.3:p.Val470=	NP_056451.3:p.Val470Ala	NP_056451.3:p.Val470Asp
translation initiation factor eIF2B subunit delta isoform 5	NP_001305895.1:p.Val456=	NP_001305895.1:p.Val456Ala	NP_001305895.1:p.Val456Asp
translation initiation factor eIF2B subunit delta isoform 4	NP_001305894.1:p.Val492=	NP_001305894.1:p.Val492Ala	NP_001305894.1:p.Val492Asp
translation initiation factor eIF2B subunit delta isoform 2	NP_001029288.1:p.Val471=	NP_001029288.1:p.Val471Ala	NP_001029288.1:p.Val471Asp
translation initiation factor eIF2B subunit delta isoform 6	NP_001305896.1:p.Val440=	NP_001305896.1:p.Val440Ala	NP_001305896.1:p.Val440Asp
translation initiation factor eIF2B subunit delta isoform 7	NP_001305897.1:p.Val276=	NP_001305897.1:p.Val276Ala	NP_001305897.1:p.Val276Asp
translation initiation factor eIF2B subunit delta isoform 8	NP_001305898.1:p.Val265=	NP_001305898.1:p.Val265Ala	NP_001305898.1:p.Val265Asp

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#.

6 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_EXAC	ss1686231639	Apr 01, 2015 (144)
2	GNOMAD	ss2732547760	Nov 08, 2017 (151)
3	GNOMAD	ss4037631007	Apr 26, 2021 (155)
4	GNOMAD	ss4037631008	Apr 26, 2021 (155)
5	TOPMED	ss4498360019	Apr 26, 2021 (155)
6	TOPMED	ss4498360020	Apr 26, 2021 (155)
7	ExAC	NC_000002.11 - 27587427	Oct 11, 2018 (152)
8	gnomAD - Genomes Submission ignored due to conflicting rows: Row 51963519 (NC_000002.12:27364559:A:G 1/140270) Row 51963520 (NC_000002.12:27364559:A:T 1/140270)	-	Apr 26, 2021 (155)
9	gnomAD - Genomes Submission ignored due to conflicting rows: Row 51963519 (NC_000002.12:27364559:A:G 1/140270) Row 51963520 (NC_000002.12:27364559:A:T 1/140270)	-	Apr 26, 2021 (155)
10	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1590655 (NC_000002.11:27587426:A:A 251487/251488, NC_000002.11:27587426:A:G 1/251488) Row 1590656 (NC_000002.11:27587426:A:A 251483/251488, NC_000002.11:27587426:A:T 5/251488)	-	Jul 13, 2019 (153)
11	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1590655 (NC_000002.11:27587426:A:A 251487/251488, NC_000002.11:27587426:A:G 1/251488) Row 1590656 (NC_000002.11:27587426:A:A 251483/251488, NC_000002.11:27587426:A:T 5/251488)	-	Jul 13, 2019 (153)
12	TopMed Submission ignored due to conflicting rows: Row 302182898 (NC_000002.12:27364559:A:G 3/264690) Row 302182899 (NC_000002.12:27364559:A:T 4/264690)	-	Apr 26, 2021 (155)
13	TopMed Submission ignored due to conflicting rows: Row 302182898 (NC_000002.12:27364559:A:G 3/264690) Row 302182899 (NC_000002.12:27364559:A:T 4/264690)	-	Apr 26, 2021 (155)
14	ALFA	NC_000002.12 - 27364560	Apr 26, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2732547760	NC_000002.11:27587426:A:G	NC_000002.12:27364559:A:G	(self)
9214309510, ss4037631007, ss4498360019	NC_000002.12:27364559:A:G	NC_000002.12:27364559:A:G	(self)
6095823, ss1686231639, ss2732547760	NC_000002.11:27587426:A:T	NC_000002.12:27364559:A:T	(self)
9214309510, ss4037631008, ss4498360020	NC_000002.12:27364559:A:T	NC_000002.12:27364559:A:T	(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 rs749983780

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

rs749983780