rs5937496

Variant names:

• chrX-76127599-G-A
• rs5937496

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 0.155 in 111,321 control chromosomes in the GnomAD database, including 1,059 homozygotes. There are 4,743 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 0.15 (1059 hom., 4743 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.155 AC: 17196 AN: 111268 Hom.: 1058 Cov.: 23 AF XY: 0.142 AC XY: 4743 AN XY: 33502

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00761

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.155 AC: 17202 AN: 111321 Hom.: 1059 Cov.: 23 AF XY: 0.141 AC XY: 4743 AN XY: 33565

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00763

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.154

Alfa AF: 0.155 Hom.: 8974

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5937496; hg19: chrX-75347434;