rs5961233

Positions:

• chrX-50904064-C-A

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 0.206 in 110,731 control chromosomes in the GnomAD database, including 2,850 homozygotes. There are 6,298 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 0.21 (2850 hom., 6298 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 22801 AN: 110678 Hom.: 2847 Cov.: 22 AF XY: 0.190 AC XY: 6269 AN XY: 32948

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.206 AC: 22842 AN: 110731 Hom.: 2850 Cov.: 22 AF XY: 0.191 AC XY: 6298 AN XY: 33011

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.193

Alfa AF: 0.143 Hom.: 2657

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961233; hg19: chrX-50647064;