X-83850275-C-T

Position:

• chrX-83850275-C-T

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 0.111 in 110,924 control chromosomes in the GnomAD database, including 696 homozygotes. There are 3,594 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 0.11 (696 hom., 3594 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

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 (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.111 AC: 12297 AN: 110871 Hom.: 699 Cov.: 22 AF XY: 0.109 AC XY: 3591 AN XY: 33089

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0929

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.111 AC: 12292 AN: 110924 Hom.: 696 Cov.: 22 AF XY: 0.108 AC XY: 3594 AN XY: 33152

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.0936

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.122 Hom.: 2135

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531868; hg19: chrX-83105283;