rs242908

Variant names:

• chrX-132605666-G-A
• rs242908

Your query was ambiguous. Multiple possible variants found:

• chrX-132605666-G-A
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;