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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1461164548

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:5892824 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/264690, TOPMED)
G=0.000005 (1/183309, GnomAD_exome)
G=0.000010 (1/103351, GnomAD) (+ 1 more)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NLGN4X : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 C=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 496 C=1.000 G=0.000 1.0 0.0 0.0 N/A


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 C=0.999996 G=0.000004
gnomAD - Exomes Global Study-wide 183309 C=0.999995 G=0.000005
gnomAD - Exomes European Sub 97830 C=0.99999 G=0.00001
gnomAD - Exomes Asian Sub 32898 C=1.00000 G=0.00000
gnomAD - Exomes American Sub 27416 C=1.00000 G=0.00000
gnomAD - Exomes African Sub 13149 C=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7488 C=1.0000 G=0.0000
gnomAD - Exomes Other Sub 4528 C=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 103351 C=0.999990 G=0.000010
gnomAD - Genomes European Sub 56851 C=0.99998 G=0.00002
gnomAD - Genomes African Sub 30972 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 9243 C=1.0000 G=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2513 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 2229 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1543 C=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 14050 C=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=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.5892824C>G
GRCh37.p13 chr X NC_000023.10:g.5810865C>G
NLGN4X RefSeqGene NG_008881.2:g.341059G>C
Gene: NLGN4X, neuroligin 4 X-linked (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NLGN4X transcript variant 2 NM_181332.3:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked precursor NP_851849.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant 3 NM_001282145.2:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked precursor NP_001269074.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant 4 NM_001282146.2:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked precursor NP_001269075.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant 1 NM_020742.4:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked precursor NP_065793.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X4 XM_006724504.3:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_006724567.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X1 XM_005274564.4:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_005274621.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X2 XM_011545547.3:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_011543849.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X3 XM_005274565.3:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_005274622.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X5 XM_005274566.5:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_005274623.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X6 XM_011545548.3:c.2504G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X1 XP_011543850.1:p.Arg835Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X7 XM_017029692.2:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X2 XP_016885181.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X8 XM_017029691.2:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X2 XP_016885180.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X9 XM_017029693.2:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X2 XP_016885182.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X10 XM_047442281.1:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X2 XP_047298237.1:p.Arg815Thr R (Arg) > T (Thr) Missense Variant
NLGN4X transcript variant X11 XM_047442282.1:c.2444G>C R [AGA] > T [ACA] Coding Sequence Variant
neuroligin-4, X-linked isoform X2 XP_047298238.1:p.Arg815Thr R (Arg) > T (Thr) 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: G (allele ID: 1293206 )
ClinVar Accession Disease Names Clinical Significance
RCV001756425.1 not provided Uncertain-Significance
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 C= G
GRCh38.p14 chr X NC_000023.11:g.5892824= NC_000023.11:g.5892824C>G
GRCh37.p13 chr X NC_000023.10:g.5810865= NC_000023.10:g.5810865C>G
NLGN4X RefSeqGene NG_008881.2:g.341059= NG_008881.2:g.341059G>C
NLGN4X transcript variant 1 NM_020742.4:c.2444= NM_020742.4:c.2444G>C
NLGN4X transcript variant 1 NM_020742.3:c.2444= NM_020742.3:c.2444G>C
NLGN4X transcript variant 1 NM_020742.2:c.2444= NM_020742.2:c.2444G>C
NLGN4X transcript variant 2 NM_181332.3:c.2444= NM_181332.3:c.2444G>C
NLGN4X transcript variant 2 NM_181332.2:c.2444= NM_181332.2:c.2444G>C
NLGN4X transcript variant 2 NM_181332.1:c.2444= NM_181332.1:c.2444G>C
NLGN4X transcript variant 3 NM_001282145.2:c.2444= NM_001282145.2:c.2444G>C
NLGN4X transcript variant 3 NM_001282145.1:c.2444= NM_001282145.1:c.2444G>C
NLGN4X transcript variant 4 NM_001282146.2:c.2444= NM_001282146.2:c.2444G>C
NLGN4X transcript variant 4 NM_001282146.1:c.2444= NM_001282146.1:c.2444G>C
NLGN4X transcript variant X5 XM_005274566.5:c.2504= XM_005274566.5:c.2504G>C
NLGN4X transcript variant X4 XM_005274566.4:c.2504= XM_005274566.4:c.2504G>C
NLGN4X transcript variant X5 XM_005274566.3:c.2504= XM_005274566.3:c.2504G>C
NLGN4X transcript variant X3 XM_005274566.2:c.2504= XM_005274566.2:c.2504G>C
NLGN4X transcript variant X3 XM_005274566.1:c.2504= XM_005274566.1:c.2504G>C
NLGN4X transcript variant X1 XM_005274564.4:c.2504= XM_005274564.4:c.2504G>C
NLGN4X transcript variant X1 XM_005274564.3:c.2504= XM_005274564.3:c.2504G>C
NLGN4X transcript variant X1 XM_005274564.2:c.2504= XM_005274564.2:c.2504G>C
NLGN4X transcript variant X1 XM_005274564.1:c.2504= XM_005274564.1:c.2504G>C
NLGN4X transcript variant X6 XM_011545548.3:c.2504= XM_011545548.3:c.2504G>C
NLGN4X transcript variant X6 XM_011545548.2:c.2504= XM_011545548.2:c.2504G>C
NLGN4X transcript variant X6 XM_011545548.1:c.2504= XM_011545548.1:c.2504G>C
NLGN4X transcript variant X2 XM_011545547.3:c.2504= XM_011545547.3:c.2504G>C
NLGN4X transcript variant X3 XM_011545547.2:c.2504= XM_011545547.2:c.2504G>C
NLGN4X transcript variant X3 XM_011545547.1:c.2504= XM_011545547.1:c.2504G>C
NLGN4X transcript variant X3 XM_005274565.3:c.2504= XM_005274565.3:c.2504G>C
NLGN4X transcript variant X2 XM_005274565.2:c.2504= XM_005274565.2:c.2504G>C
NLGN4X transcript variant X2 XM_005274565.1:c.2504= XM_005274565.1:c.2504G>C
NLGN4X transcript variant X4 XM_006724504.3:c.2504= XM_006724504.3:c.2504G>C
NLGN4X transcript variant X4 XM_006724504.2:c.2504= XM_006724504.2:c.2504G>C
NLGN4X transcript variant X6 XM_006724504.1:c.2504= XM_006724504.1:c.2504G>C
NLGN4X transcript variant X7 XM_017029692.2:c.2444= XM_017029692.2:c.2444G>C
NLGN4X transcript variant X8 XM_017029692.1:c.2444= XM_017029692.1:c.2444G>C
NLGN4X transcript variant X9 XM_017029693.2:c.2444= XM_017029693.2:c.2444G>C
NLGN4X transcript variant X9 XM_017029693.1:c.2444= XM_017029693.1:c.2444G>C
NLGN4X transcript variant X8 XM_017029691.2:c.2444= XM_017029691.2:c.2444G>C
NLGN4X transcript variant X7 XM_017029691.1:c.2444= XM_017029691.1:c.2444G>C
NLGN4X transcript variant X10 XM_047442281.1:c.2444= XM_047442281.1:c.2444G>C
NLGN4X transcript variant X11 XM_047442282.1:c.2444= XM_047442282.1:c.2444G>C
neuroligin-4, X-linked precursor NP_065793.1:p.Arg815= NP_065793.1:p.Arg815Thr
neuroligin-4, X-linked precursor NP_851849.1:p.Arg815= NP_851849.1:p.Arg815Thr
neuroligin-4, X-linked precursor NP_001269074.1:p.Arg815= NP_001269074.1:p.Arg815Thr
neuroligin-4, X-linked precursor NP_001269075.1:p.Arg815= NP_001269075.1:p.Arg815Thr
neuroligin-4, X-linked isoform X1 XP_005274623.1:p.Arg835= XP_005274623.1:p.Arg835Thr
neuroligin-4, X-linked isoform X1 XP_005274621.1:p.Arg835= XP_005274621.1:p.Arg835Thr
neuroligin-4, X-linked isoform X1 XP_011543850.1:p.Arg835= XP_011543850.1:p.Arg835Thr
neuroligin-4, X-linked isoform X1 XP_011543849.1:p.Arg835= XP_011543849.1:p.Arg835Thr
neuroligin-4, X-linked isoform X1 XP_005274622.1:p.Arg835= XP_005274622.1:p.Arg835Thr
neuroligin-4, X-linked isoform X1 XP_006724567.1:p.Arg835= XP_006724567.1:p.Arg835Thr
neuroligin-4, X-linked isoform X2 XP_016885181.1:p.Arg815= XP_016885181.1:p.Arg815Thr
neuroligin-4, X-linked isoform X2 XP_016885182.1:p.Arg815= XP_016885182.1:p.Arg815Thr
neuroligin-4, X-linked isoform X2 XP_016885180.1:p.Arg815= XP_016885180.1:p.Arg815Thr
neuroligin-4, X-linked isoform X2 XP_047298237.1:p.Arg815= XP_047298237.1:p.Arg815Thr
neuroligin-4, X-linked isoform X2 XP_047298238.1:p.Arg815= XP_047298238.1:p.Arg815Thr
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#.

3 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2745296119 Nov 08, 2017 (151)
2 GNOMAD ss4367598109 Apr 26, 2021 (155)
3 TOPMED ss5114650150 Apr 26, 2021 (155)
4 gnomAD - Genomes NC_000023.11 - 5892824 Apr 26, 2021 (155)
5 gnomAD - Exomes NC_000023.10 - 5810865 Jul 13, 2019 (153)
6 TopMed NC_000023.11 - 5892824 Apr 26, 2021 (155)
7 ALFA NC_000023.11 - 5892824 Apr 26, 2021 (155)
8 ClinVar RCV001756425.1 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
14632661, ss2745296119 NC_000023.10:5810864:C:G NC_000023.11:5892823:C:G (self)
RCV001756425.1, 574592656, 678256507, 9677947989, ss4367598109, ss5114650150 NC_000023.11:5892823:C:G NC_000023.11:5892823:C:G (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 rs1461164548

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.post820+afb47a3d