X-76138369-T-C

Position:

• chrX-76138369-T-C

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 0.455 in 110,771 control chromosomes in the GnomAD database, including 9,554 homozygotes. There are 14,689 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 0.46 (9554 hom., 14689 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

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 (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.455 AC: 50418 AN: 110718 Hom.: 9563 Cov.: 22 AF XY: 0.445 AC XY: 14670 AN XY: 32938

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.455 AC: 50415 AN: 110771 Hom.: 9554 Cov.: 22 AF XY: 0.445 AC XY: 14689 AN XY: 33001

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.505

Alfa AF: 0.553 Hom.: 16043

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4892427; hg19: chrX-75358204;