X-5014524-C-T

Variant names:

• chrX-5014524-C-T
• rs5961595

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 8046 AN: 109980 Hom.: 307 Cov.: 21

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

African (AFR) AF: 0.132 AC: 3985 AN: 30221

American (AMR) AF: 0.0715 AC: 732 AN: 10243

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 49 AN: 2626

East Asian (EAS) AF: 0.000574 AC: 2 AN: 3483

South Asian (SAS) AF: 0.00823 AC: 21 AN: 2552

European-Finnish (FIN) AF: 0.0572 AC: 330 AN: 5766

Middle Eastern (MID) AF: 0.0333 AC: 7 AN: 210

European-Non Finnish (NFE) AF: 0.0532 AC: 2805 AN: 52748

Other (OTH) AF: 0.0700 AC: 105 AN: 1500

Alfa AF: 0.0587 Hom.: 2523

Bravo AF: 0.0799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.33
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs5961595; hg19: chrX-4932565;