X-50904064-C-A

Variant names:

• chrX-50904064-C-A
• rs5961233

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 0.206 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 22801 AN: 110678 Hom.: 2847 Cov.: 22

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

African (AFR) AF: 0.463 AC: 14019 AN: 30267

American (AMR) AF: 0.0939 AC: 984 AN: 10483

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 387 AN: 2632

East Asian (EAS) AF: 0.0487 AC: 172 AN: 3533

South Asian (SAS) AF: 0.159 AC: 408 AN: 2564

European-Finnish (FIN) AF: 0.119 AC: 701 AN: 5886

Middle Eastern (MID) AF: 0.197 AC: 42 AN: 213

European-Non Finnish (NFE) AF: 0.110 AC: 5810 AN: 52961

Other (OTH) AF: 0.193 AC: 292 AN: 1511

Alfa AF: 0.193 Hom.: 6742

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5961233; hg19: chrX-50647064;