rs6639932

Variant names:

• chrX-4388236-A-G
• rs6639932

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.105 in 110,366 control chromosomes in the GnomAD database, including 1,180 homozygotes. There are 3,179 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 0.10 (1180 hom., 3179 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.104 AC: 11514 AN: 110320 Hom.: 1174 Cov.: 22 AF XY: 0.0970 AC XY: 3162 AN XY: 32586

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0339

Gnomad NFE AF: 0.00415

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.105 AC: 11547 AN: 110366 Hom.: 1180 Cov.: 22 AF XY: 0.0974 AC XY: 3179 AN XY: 32642

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0853

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.00415

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0667 Hom.: 368

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6639932; hg19: chrX-4306277;