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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.

rs782555986

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:154354904 (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=0.000042 (11/264690, TOPMED)
A=0.000033 (6/181235, GnomAD_exome)
A=0.000038 (4/105389, GnomAD) (+ 2 more)
A=0.00005 (4/85938, ExAC)
A=0.00014 (2/14050, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
FLNA : 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 14050 G=0.99986 A=0.00014
European Sub 9690 G=0.9998 A=0.0002
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=0.000


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 G=0.999958 A=0.000042
gnomAD - Exomes Global Study-wide 181235 G=0.999967 A=0.000033
gnomAD - Exomes European Sub 97006 G=0.99998 A=0.00002
gnomAD - Exomes Asian Sub 32593 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 27365 G=0.99996 A=0.00004
gnomAD - Exomes African Sub 12351 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7459 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4461 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 105389 G=0.999962 A=0.000038
gnomAD - Genomes European Sub 57543 G=0.99995 A=0.00005
gnomAD - Genomes African Sub 31829 G=0.99997 A=0.00003
gnomAD - Genomes American Sub 9627 G=1.0000 A=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2532 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2252 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1606 G=1.0000 A=0.0000
ExAC Global Study-wide 85938 G=0.99995 A=0.00005
ExAC Europe Sub 51593 G=1.00000 A=0.00000
ExAC Asian Sub 16646 G=0.99988 A=0.00012
ExAC American Sub 9276 G=0.9999 A=0.0001
ExAC African Sub 7807 G=1.0000 A=0.0000
ExAC Other Sub 616 G=0.998 A=0.002
Allele Frequency Aggregator Total Global 14050 G=0.99986 A=0.00014
Allele Frequency Aggregator European Sub 9690 G=0.9998 A=0.0002
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
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 X NC_000023.11:g.154354904G>A
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1788883G>A
FLNA RefSeqGene (LRG_1340) NG_011506.2:g.24735C>T
GRCh37.p13 chr X NC_000023.10:g.153583272G>A
Gene: FLNA, filamin A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FLNA transcript variant 2 NM_001110556.2:c.5138C>T T [ACG] > M [ATG] Coding Sequence Variant
filamin-A isoform 2 NP_001104026.1:p.Thr1713M…

NP_001104026.1:p.Thr1713Met

T (Thr) > M (Met) Missense Variant
FLNA transcript variant 1 NM_001456.4:c.5114C>T T [ACG] > M [ATG] Coding Sequence Variant
filamin-A isoform 1 NP_001447.2:p.Thr1705Met T (Thr) > M (Met) Missense 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: A (allele ID: 446570 )
ClinVar Accession Disease Names Clinical Significance
RCV000520883.3 not provided Uncertain-Significance
RCV001084701.4 Frontometaphyseal dysplasia,Heterotopia, periventricular, X-linked dominant,Melnick-Needles syndrome,Oto-palato-digital syndrome, type II Likely-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 G= A
GRCh38.p14 chr X NC_000023.11:g.154354904= NC_000023.11:g.154354904G>A
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1788883= NW_003871103.3:g.1788883G>A
FLNA RefSeqGene (LRG_1340) NG_011506.2:g.24735= NG_011506.2:g.24735C>T
FLNA transcript variant 1 NM_001456.4:c.5114= NM_001456.4:c.5114C>T
FLNA transcript variant 1 NM_001456.3:c.5114= NM_001456.3:c.5114C>T
FLNA transcript variant 2 NM_001110556.2:c.5138= NM_001110556.2:c.5138C>T
FLNA transcript variant 2 NM_001110556.1:c.5138= NM_001110556.1:c.5138C>T
GRCh37.p13 chr X NC_000023.10:g.153583272= NC_000023.10:g.153583272G>A
filamin-A isoform 1 NP_001447.2:p.Thr1705= NP_001447.2:p.Thr1705Met
filamin-A isoform 2 NP_001104026.1:p.Thr1713= NP_001104026.1:p.Thr1713Met
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#.

7 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1694657038 Apr 09, 2015 (144)
2 HUMAN_LONGEVITY ss2321317402 Dec 20, 2016 (150)
3 GNOMAD ss2745616756 Oct 13, 2018 (152)
4 GNOMAD ss2746163782 Oct 13, 2018 (152)
5 GNOMAD ss2984744368 Oct 13, 2018 (152)
6 GNOMAD ss4381171186 Apr 26, 2021 (155)
7 TOPMED ss5141577899 Apr 26, 2021 (155)
8 ExAC NC_000023.10 - 153583272 Oct 13, 2018 (152)
9 gnomAD - Genomes NC_000023.11 - 154354904 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000023.10 - 153583272 Jul 14, 2019 (153)
11 TopMed NC_000023.11 - 154354904 Apr 26, 2021 (155)
12 ALFA NC_000023.11 - 154354904 Apr 26, 2021 (155)
13 ClinVar RCV000520883.3 Apr 26, 2021 (155)
14 ClinVar RCV001084701.4 Oct 17, 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
10168592, 14946101, ss1694657038, ss2745616756, ss2746163782, ss2984744368 NC_000023.10:153583271:G:A NC_000023.11:154354903:G:A (self)
RCV000520883.3, RCV001084701.4, 594538048, 705184256, 4246396565, ss2321317402, ss4381171186, ss5141577899 NC_000023.11:154354903:G:A NC_000023.11:154354903:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs782555986

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