X-5014524-C-T

Variant names:

• chrX-5014524-C-T
• rs5961595

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 0.0732 in 110,031 control chromosomes in the GnomAD database, including 307 homozygotes. There are 2,140 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 0.073 (307 hom., 2140 hem., cov: 21)
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 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: 0.0732 AC: 8046 AN: 109980 Hom.: 307 Cov.: 21 AF XY: 0.0661 AC XY: 2136 AN XY: 32298

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0279

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.000572

Gnomad SAS AF: 0.00821

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0343

Gnomad NFE AF: 0.0532

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0732 AC: 8055 AN: 110031 Hom.: 307 Cov.: 21 AF XY: 0.0661 AC XY: 2140 AN XY: 32359

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.000574

Gnomad4 SAS AF: 0.00823

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.0532

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0523 Hom.: 1812

Bravo AF: 0.0799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961595; hg19: chrX-4932565;