rs242908

chrX-132605666-G-AchrX-132605666-G-T

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 0.543 in 110,577 control chromosomes in the GnomAD database, including 13,732 homozygotes. There are 17,292 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 0.54 (13732 hom., 17292 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.543 AC: 60019 AN: 110519 Hom.: 13724 Cov.: 22 AF XY: 0.526 AC XY: 17240 AN XY: 32749

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.543 AC: 60072 AN: 110577 Hom.: 13732 Cov.: 22 AF XY: 0.527 AC XY: 17292 AN XY: 32817

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.528

Alfa AF: 0.427 Hom.: 32112

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.5
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242908; hg19: chrX-131739694;