rs764908

Variant names:

• chrX-149295812-G-A
• rs764908

Your query was ambiguous. Multiple possible variants found:

• chrX-149295812-G-A
• chrX-149295812-G-C
• chrX-149295812-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.528 AC: 58159 AN: 110170 Hom.: 12354 Cov.: 22 AF XY: 0.529 AC XY: 17155 AN XY: 32456

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.583

Alfa AF: 0.610 Hom.: 34643

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764908; hg19: chrX-148377342;