X-83161825-A-G

Position:

• chrX-83161825-A-G

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 0.259 in 110,489 control chromosomes in the GnomAD database, including 3,266 homozygotes. There are 8,171 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 0.26 (3266 hom., 8171 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 28554 AN: 110441 Hom.: 3262 Cov.: 22 AF XY: 0.249 AC XY: 8141 AN XY: 32729

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.0966

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.251

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.259 AC: 28585 AN: 110489 Hom.: 3266 Cov.: 22 AF XY: 0.249 AC XY: 8171 AN XY: 32787

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.260

Alfa AF: 0.196 Hom.: 3414

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
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: rs210453; hg19: chrX-82416833;