Name: rs747918225
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.

rs747918225

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:93740620 (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: T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.000007 (1/139604, GnomAD)
C=0.00000 (0/10680, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: POU5F2 : Missense Variant
FAM172A : 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	10680	T=1.00000	C=0.00000
European	Sub	6962	T=1.0000	C=0.0000
African	Sub	2294	T=1.0000	C=0.0000
African Others	Sub	84	T=1.00	C=0.00
African American	Sub	2210	T=1.0000	C=0.0000
Asian	Sub	108	T=1.000	C=0.000
East Asian	Sub	84	T=1.00	C=0.00
Other Asian	Sub	24	T=1.00	C=0.00
Latin American 1	Sub	146	T=1.000	C=0.000
Latin American 2	Sub	610	T=1.000	C=0.000
South Asian	Sub	94	T=1.00	C=0.00
Other	Sub	466	T=1.000	C=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
gnomAD - Genomes	Global	Study-wide	139604	T=0.999993	C=0.000007
gnomAD - Genomes	European	Sub	75660	T=1.00000	C=0.00000
gnomAD - Genomes	African	Sub	41776	T=0.99998	C=0.00002
gnomAD - Genomes	American	Sub	13592	T=1.00000	C=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3120	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2136	T=1.0000	C=0.0000
Allele Frequency Aggregator	Total	Global	10680	T=1.00000	C=0.00000
Allele Frequency Aggregator	European	Sub	6962	T=1.0000	C=0.0000
Allele Frequency Aggregator	African	Sub	2294	T=1.0000	C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	T=1.000	C=0.000
Allele Frequency Aggregator	Other	Sub	466	T=1.000	C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=1.000	C=0.000
Allele Frequency Aggregator	Asian	Sub	108	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	94	T=1.00	C=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 5	NC_000005.10:g.93740620T>C
GRCh38.p14 chr 5	NC_000005.10:g.93740620T>G
GRCh37.p13 chr 5	NC_000005.9:g.93076326T>C
GRCh37.p13 chr 5	NC_000005.9:g.93076326T>G

Gene: FAM172A, family with sequence similarity 172 member A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARB2A transcript variant 2	NM_001163417.1:c.970+3553… NM_001163417.1:c.970+35539A>G	N/A	Intron Variant
ARB2A transcript variant 3	NM_001163418.1:c.778+3553… NM_001163418.1:c.778+35539A>G	N/A	Intron Variant
ARB2A transcript variant 1	NM_032042.6:c.1108+35539A… NM_032042.6:c.1108+35539A>G	N/A	Intron Variant
ARB2A transcript variant 4	NR_028080.1:n.	N/A	Intron Variant
ARB2A transcript variant X11	XM_005272105.5:c.916+3553… XM_005272105.5:c.916+35539A>G	N/A	Intron Variant
ARB2A transcript variant X13	XM_005272106.5:c.889+3553… XM_005272106.5:c.889+35539A>G	N/A	Intron Variant
ARB2A transcript variant X25	XM_005272110.4:c.751+3553… XM_005272110.4:c.751+35539A>G	N/A	Intron Variant
ARB2A transcript variant X1	XM_006714717.4:c.1108+355… XM_006714717.4:c.1108+35539A>G	N/A	Intron Variant
ARB2A transcript variant X19	XM_006714718.4:c.859+3553… XM_006714718.4:c.859+35539A>G	N/A	Intron Variant
ARB2A transcript variant X7	XM_011543671.4:c.1108+355… XM_011543671.4:c.1108+35539A>G	N/A	Intron Variant
ARB2A transcript variant X2	XM_017009953.2:c.1042+355… XM_017009953.2:c.1042+35539A>G	N/A	Intron Variant
ARB2A transcript variant X9	XM_017009955.2:c.970+3553… XM_017009955.2:c.970+35539A>G	N/A	Intron Variant
ARB2A transcript variant X18	XM_017009957.2:c.859+3553… XM_017009957.2:c.859+35539A>G	N/A	Intron Variant
ARB2A transcript variant X20	XM_017009958.2:c.859+3553… XM_017009958.2:c.859+35539A>G	N/A	Intron Variant
ARB2A transcript variant X8	XM_047417810.1:c.970+3553… XM_047417810.1:c.970+35539A>G	N/A	Intron Variant
ARB2A transcript variant X10	XM_047417811.1:c.1108+355… XM_047417811.1:c.1108+35539A>G	N/A	Intron Variant
ARB2A transcript variant X16	XM_047417814.1:c.859+3553… XM_047417814.1:c.859+35539A>G	N/A	Intron Variant
ARB2A transcript variant X17	XM_047417815.1:c.859+3553… XM_047417815.1:c.859+35539A>G	N/A	Intron Variant
ARB2A transcript variant X22	XM_047417817.1:c.889+3553… XM_047417817.1:c.889+35539A>G	N/A	Intron Variant
ARB2A transcript variant X24	XM_047417818.1:c.823+3553… XM_047417818.1:c.823+35539A>G	N/A	Intron Variant
ARB2A transcript variant X28	XM_047417820.1:c.667+3553… XM_047417820.1:c.667+35539A>G	N/A	Intron Variant
ARB2A transcript variant X4	XM_005272103.5:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X23	XM_005272109.6:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X27	XM_005272111.6:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X5	XM_011543668.4:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X6	XM_011543670.4:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X3	XM_017009954.3:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X30	XM_017009961.3:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X31	XM_017009962.2:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X14	XM_047417812.1:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X15	XM_047417813.1:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X21	XM_047417816.1:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X26	XM_047417819.1:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X29	XM_047417822.1:c.	N/A	Genic Downstream Transcript Variant
ARB2A transcript variant X12	XR_007058646.1:n.	N/A	Genic Downstream Transcript Variant

Gene: POU5F2, POU domain class 5, transcription factor 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
POU5F2 transcript	NM_153216.2:c.944A>G	H [CAC] > R [CGC]	Coding Sequence Variant
POU domain, class 5, transcription factor 2	NP_694948.1:p.His315Arg	H (His) > R (Arg)	Missense Variant
POU5F2 transcript	NM_153216.2:c.944A>C	H [CAC] > P [CCC]	Coding Sequence Variant
POU domain, class 5, transcription factor 2	NP_694948.1:p.His315Pro	H (His) > P (Pro)	Missense 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	T=	C	G
GRCh38.p14 chr 5	NC_000005.10:g.93740620=	NC_000005.10:g.93740620T>C	NC_000005.10:g.93740620T>G
GRCh37.p13 chr 5	NC_000005.9:g.93076326=	NC_000005.9:g.93076326T>C	NC_000005.9:g.93076326T>G
POU5F2 transcript	NM_153216.2:c.944=	NM_153216.2:c.944A>G	NM_153216.2:c.944A>C
POU5F2 transcript	NM_153216.1:c.944=	NM_153216.1:c.944A>G	NM_153216.1:c.944A>C
POU domain, class 5, transcription factor 2	NP_694948.1:p.His315=	NP_694948.1:p.His315Arg	NP_694948.1:p.His315Pro
ARB2A transcript variant 2	NM_001163417.1:c.970+35539=	NM_001163417.1:c.970+35539A>G	NM_001163417.1:c.970+35539A>C
ARB2A transcript variant 3	NM_001163418.1:c.778+35539=	NM_001163418.1:c.778+35539A>G	NM_001163418.1:c.778+35539A>C
FAM172A transcript variant 1	NM_032042.5:c.1108+35539=	NM_032042.5:c.1108+35539A>G	NM_032042.5:c.1108+35539A>C
ARB2A transcript variant 1	NM_032042.6:c.1108+35539=	NM_032042.6:c.1108+35539A>G	NM_032042.6:c.1108+35539A>C
FAM172A transcript variant X2	XM_005272104.1:c.970+35539=	XM_005272104.1:c.970+35539A>G	XM_005272104.1:c.970+35539A>C
FAM172A transcript variant X3	XM_005272105.1:c.916+35539=	XM_005272105.1:c.916+35539A>G	XM_005272105.1:c.916+35539A>C
ARB2A transcript variant X11	XM_005272105.5:c.916+35539=	XM_005272105.5:c.916+35539A>G	XM_005272105.5:c.916+35539A>C
FAM172A transcript variant X4	XM_005272106.1:c.889+35539=	XM_005272106.1:c.889+35539A>G	XM_005272106.1:c.889+35539A>C
ARB2A transcript variant X13	XM_005272106.5:c.889+35539=	XM_005272106.5:c.889+35539A>G	XM_005272106.5:c.889+35539A>C
FAM172A transcript variant X6	XM_005272108.1:c.859+35539=	XM_005272108.1:c.859+35539A>G	XM_005272108.1:c.859+35539A>C
FAM172A transcript variant X8	XM_005272110.1:c.751+35539=	XM_005272110.1:c.751+35539A>G	XM_005272110.1:c.751+35539A>C
ARB2A transcript variant X25	XM_005272110.4:c.751+35539=	XM_005272110.4:c.751+35539A>G	XM_005272110.4:c.751+35539A>C
FAM172A transcript variant X10	XM_005272112.1:c.667+35539=	XM_005272112.1:c.667+35539A>G	XM_005272112.1:c.667+35539A>C
ARB2A transcript variant X1	XM_006714717.4:c.1108+35539=	XM_006714717.4:c.1108+35539A>G	XM_006714717.4:c.1108+35539A>C
ARB2A transcript variant X19	XM_006714718.4:c.859+35539=	XM_006714718.4:c.859+35539A>G	XM_006714718.4:c.859+35539A>C
ARB2A transcript variant X7	XM_011543671.4:c.1108+35539=	XM_011543671.4:c.1108+35539A>G	XM_011543671.4:c.1108+35539A>C
ARB2A transcript variant X2	XM_017009953.2:c.1042+35539=	XM_017009953.2:c.1042+35539A>G	XM_017009953.2:c.1042+35539A>C
ARB2A transcript variant X9	XM_017009955.2:c.970+35539=	XM_017009955.2:c.970+35539A>G	XM_017009955.2:c.970+35539A>C
ARB2A transcript variant X18	XM_017009957.2:c.859+35539=	XM_017009957.2:c.859+35539A>G	XM_017009957.2:c.859+35539A>C
ARB2A transcript variant X20	XM_017009958.2:c.859+35539=	XM_017009958.2:c.859+35539A>G	XM_017009958.2:c.859+35539A>C
ARB2A transcript variant X8	XM_047417810.1:c.970+35539=	XM_047417810.1:c.970+35539A>G	XM_047417810.1:c.970+35539A>C
ARB2A transcript variant X10	XM_047417811.1:c.1108+35539=	XM_047417811.1:c.1108+35539A>G	XM_047417811.1:c.1108+35539A>C
ARB2A transcript variant X16	XM_047417814.1:c.859+35539=	XM_047417814.1:c.859+35539A>G	XM_047417814.1:c.859+35539A>C
ARB2A transcript variant X17	XM_047417815.1:c.859+35539=	XM_047417815.1:c.859+35539A>G	XM_047417815.1:c.859+35539A>C
ARB2A transcript variant X22	XM_047417817.1:c.889+35539=	XM_047417817.1:c.889+35539A>G	XM_047417817.1:c.889+35539A>C
ARB2A transcript variant X24	XM_047417818.1:c.823+35539=	XM_047417818.1:c.823+35539A>G	XM_047417818.1:c.823+35539A>C
ARB2A transcript variant X28	XM_047417820.1:c.667+35539=	XM_047417820.1:c.667+35539A>G	XM_047417820.1:c.667+35539A>C

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#.

4 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_EXAC	ss1687883386	Apr 01, 2015 (144)
2	EVA_EXAC	ss1687883387	Apr 01, 2015 (144)
3	GNOMAD	ss2735117908	Nov 08, 2017 (151)
4	GNOMAD	ss4108967878	Apr 26, 2021 (155)
5	ExAC Submission ignored due to conflicting rows: Row 7880849 (NC_000005.9:93076325:T:T 117967/117968, NC_000005.9:93076325:T:C 1/117968) Row 7880850 (NC_000005.9:93076325:T:T 117967/117968, NC_000005.9:93076325:T:G 1/117968)	-	Oct 12, 2018 (152)
6	ExAC Submission ignored due to conflicting rows: Row 7880849 (NC_000005.9:93076325:T:T 117967/117968, NC_000005.9:93076325:T:C 1/117968) Row 7880850 (NC_000005.9:93076325:T:T 117967/117968, NC_000005.9:93076325:T:G 1/117968)	-	Oct 12, 2018 (152)
7	gnomAD - Genomes	NC_000005.10 - 93740620	Apr 26, 2021 (155)
8	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4237737 (NC_000005.9:93076325:T:T 248271/248272, NC_000005.9:93076325:T:C 1/248272) Row 4237738 (NC_000005.9:93076325:T:T 248271/248272, NC_000005.9:93076325:T:G 1/248272)	-	Jul 13, 2019 (153)
9	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4237737 (NC_000005.9:93076325:T:T 248271/248272, NC_000005.9:93076325:T:C 1/248272) Row 4237738 (NC_000005.9:93076325:T:T 248271/248272, NC_000005.9:93076325:T:G 1/248272)	-	Jul 13, 2019 (153)
10	ALFA	NC_000005.10 - 93740620	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
ss1687883386, ss2735117908	NC_000005.9:93076325:T:C	NC_000005.10:93740619:T:C	(self)
196170506, 4421514229, ss4108967878	NC_000005.10:93740619:T:C	NC_000005.10:93740619:T:C	(self)
ss1687883387, ss2735117908	NC_000005.9:93076325:T:G	NC_000005.10:93740619:T:G	(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 rs747918225

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

rs747918225