X-50907893-T-A

Position:

• chrX-50907893-T-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 0.191 in 103,289 control chromosomes in the GnomAD database, including 2,770 homozygotes. There are 5,152 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 0.19 (2770 hom., 5152 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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: 0.190 AC: 19660 AN: 103235 Hom.: 2767 Cov.: 22 AF XY: 0.180 AC XY: 5123 AN XY: 28423

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0304

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.191 AC: 19704 AN: 103289 Hom.: 2770 Cov.: 22 AF XY: 0.181 AC XY: 5152 AN XY: 28477

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.164

Alfa AF: 0.119 Hom.: 704

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857030; hg19: chrX-50650893;