chrX-149295812-G-A

Variant names:

• chrX-149295812-G-A
• rs764908

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.528 in 110,221 control chromosomes in the GnomAD database, including 12,356 homozygotes. There are 17,165 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 0.53 (12356 hom., 17165 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 58159 AN: 110170 Hom.: 12354 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.528 AC: 58160 AN: 110221 Hom.: 12356 Cov.: 22 AF XY: 0.528 AC XY: 17165 AN XY: 32517

African (AFR) AF: 0.217 AC: 6606 AN: 30378

American (AMR) AF: 0.729 AC: 7535 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 1721 AN: 2627

East Asian (EAS) AF: 0.806 AC: 2780 AN: 3448

South Asian (SAS) AF: 0.708 AC: 1800 AN: 2541

European-Finnish (FIN) AF: 0.566 AC: 3283 AN: 5804

Middle Eastern (MID) AF: 0.636 AC: 138 AN: 217

European-Non Finnish (NFE) AF: 0.626 AC: 33015 AN: 52700

Other (OTH) AF: 0.583 AC: 877 AN: 1505

Alfa AF: 0.594 Hom.: 51457

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	20
DANN	Benign	0.78
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs764908; hg19: chrX-148377342;