Name: rs1373009715
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.

rs1373009715

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:189961856-189961859 (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: delA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.000004 (1/264690, TOPMED)
delA=0.000008 (2/236078, GnomAD_exome)
delA=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FRG1 : Stop Gained
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HWEP
Total	Global	14050	AAAA=1.00000	AAA=0.00000	1.0	N/A
European	Sub	9690	AAAA=1.0000	AAA=0.0000	1.0	N/A
African	Sub	2898	AAAA=1.0000	AAA=0.0000	1.0	N/A
African Others	Sub	114	AAAA=1.000	AAA=0.000	1.0	N/A
African American	Sub	2784	AAAA=1.0000	AAA=0.0000	1.0	N/A
Asian	Sub	112	AAAA=1.000	AAA=0.000	1.0	N/A
East Asian	Sub	86	AAAA=1.00	AAA=0.00	1.0	N/A
Other Asian	Sub	26	AAAA=1.00	AAA=0.00	1.0	N/A
Latin American 1	Sub	146	AAAA=1.000	AAA=0.000	1.0	N/A
Latin American 2	Sub	610	AAAA=1.000	AAA=0.000	1.0	N/A
South Asian	Sub	98	AAAA=1.00	AAA=0.00	1.0	N/A
Other	Sub	496	AAAA=1.000	AAA=0.000	1.0	N/A

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	(A)₄=0.999996	delA=0.000004
gnomAD - Exomes	Global	Study-wide	236078	(A)₄=0.999992	delA=0.000008
gnomAD - Exomes	European	Sub	130380	(A)₄=0.999985	delA=0.000015
gnomAD - Exomes	Asian	Sub	44448	(A)₄=1.00000	delA=0.00000
gnomAD - Exomes	American	Sub	31454	(A)₄=1.00000	delA=0.00000
gnomAD - Exomes	African	Sub	14360	(A)₄=1.00000	delA=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9660	(A)₄=1.0000	delA=0.0000
gnomAD - Exomes	Other	Sub	5776	(A)₄=1.0000	delA=0.0000
Allele Frequency Aggregator	Total	Global	14050	(A)₄=1.00000	delA=0.00000
Allele Frequency Aggregator	European	Sub	9690	(A)₄=1.0000	delA=0.0000
Allele Frequency Aggregator	African	Sub	2898	(A)₄=1.0000	delA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₄=1.000	delA=0.000
Allele Frequency Aggregator	Other	Sub	496	(A)₄=1.000	delA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₄=1.000	delA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₄=1.000	delA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₄=1.00	delA=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 4	NC_000004.12:g.189961859del
GRCh37.p13 chr 4	NC_000004.11:g.190883014del
FRG1 RefSeqGene	NG_008142.1:g.26041del
GRCh38.p14 chr 4 novel patch HSCHR4_11_CTG12	NW_015495301.1:g.54789del
GRCh37.p13 chr 4 fix patch HG1032_PATCH	NW_003571034.1:g.54789del
GRCh38.p14 chr 4 fix patch HG2023_PATCH	NW_015495300.1:g.54789del
GRCh38.p14 chr 4 alt locus HSCHR4_6_CTG12	NT_187650.1:g.299390del

Gene: FRG1, FSHD region gene 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FRG1 transcript	NM_004477.3:c.667del	I [ATA] > * [TA]	Coding Sequence Variant
protein FRG1	NP_004468.1:p.Lys222_Ile2… NP_004468.1:p.Lys222_Ile223insTer	I (Ile) > * (Ter)	Stop Gained
FRG1 transcript variant X1	XM_017007958.2:c.283del	I [ATA] > * [TA]	Coding Sequence Variant
protein FRG1 isoform X1	XP_016863447.1:p.Lys94_Il… XP_016863447.1:p.Lys94_Ile95insTer	I (Ile) > * (Ter)	Stop Gained

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)₄=	delA
GRCh38.p14 chr 4	NC_000004.12:g.189961856_189961859=	NC_000004.12:g.189961859del
GRCh37.p13 chr 4	NC_000004.11:g.190883011_190883014=	NC_000004.11:g.190883014del
FRG1 RefSeqGene	NG_008142.1:g.26038_26041=	NG_008142.1:g.26041del
FRG1 transcript	NM_004477.3:c.664_667=	NM_004477.3:c.667del
FRG1 transcript	NM_004477.2:c.664_667=	NM_004477.2:c.667del
GRCh38.p14 chr 4 novel patch HSCHR4_11_CTG12	NW_015495301.1:g.54786_54789=	NW_015495301.1:g.54789del
GRCh37.p13 chr 4 fix patch HG1032_PATCH	NW_003571034.1:g.54786_54789=	NW_003571034.1:g.54789del
GRCh38.p14 chr 4 fix patch HG2023_PATCH	NW_015495300.1:g.54786_54789=	NW_015495300.1:g.54789del
GRCh38.p14 chr 4 alt locus HSCHR4_6_CTG12	NT_187650.1:g.299387_299390=	NT_187650.1:g.299390del
FRG1 transcript variant X1	XM_017007958.2:c.280_283=	XM_017007958.2:c.283del
FRG1 transcript variant X2	XM_017007958.1:c.280_283=	XM_017007958.1:c.283del
protein FRG1	NP_004468.1:p.Lys222_Ile223=	NP_004468.1:p.Lys222_Ile223insTer
protein FRG1 isoform X1	XP_016863447.1:p.Lys94_Ile95=	XP_016863447.1:p.Lys94_Ile95insTer

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#.

2 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2734866719	Nov 08, 2017 (151)
2	TOPMED	ss4646789045	Apr 26, 2021 (155)
3	gnomAD - Exomes	NC_000004.11 - 190883011	Jul 13, 2019 (153)
4	TopMed	NC_000004.12 - 189961856	Apr 26, 2021 (155)
5	ALFA	NC_000004.12 - 189961856	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
3981149, ss2734866719	NC_000004.11:190883010:A:	NC_000004.12:189961855:AAAA:AAA	(self)
484166601, ss4646789045	NC_000004.12:189961855:A:	NC_000004.12:189961855:AAAA:AAA	(self)
1701356918	NC_000004.12:189961855:AAAA:AAA	NC_000004.12:189961855:AAAA:AAA	(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 rs1373009715

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

rs1373009715