rs2495637

Variant names:

• chrX-118726116-G-A
• rs2495637

Your query was ambiguous. Multiple possible variants found:

• chrX-118726116-G-A
• chrX-118726116-G-C
• chrX-118726116-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.178 in 110,877 control chromosomes in the GnomAD database, including 1,539 homozygotes. There are 6,195 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (1539 hom., 6195 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.178 AC: 19683 AN: 110825 Hom.: 1540 Cov.: 22

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.178 AC: 19702 AN: 110877 Hom.: 1539 Cov.: 22 AF XY: 0.187 AC XY: 6195 AN XY: 33117

African (AFR) AF: 0.0928 AC: 2838 AN: 30567

American (AMR) AF: 0.357 AC: 3701 AN: 10380

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 644 AN: 2627

East Asian (EAS) AF: 0.409 AC: 1423 AN: 3475

South Asian (SAS) AF: 0.308 AC: 807 AN: 2621

European-Finnish (FIN) AF: 0.198 AC: 1152 AN: 5818

Middle Eastern (MID) AF: 0.300 AC: 64 AN: 213

European-Non Finnish (NFE) AF: 0.164 AC: 8700 AN: 52982

Other (OTH) AF: 0.225 AC: 341 AN: 1514

Alfa AF: 0.169 Hom.: 8435

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2495637; hg19: chrX-117860079;