rs6639932

chrX-4388236-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;