rs2213392

Positions:

• chrX-102017519-G-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 0.394 in 110,791 control chromosomes in the GnomAD database, including 6,566 homozygotes. There are 12,438 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 0.39 (6566 hom., 12438 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.394 AC: 43601 AN: 110737 Hom.: 6565 Cov.: 23 AF XY: 0.376 AC XY: 12414 AN XY: 32987

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.394 AC: 43618 AN: 110791 Hom.: 6566 Cov.: 23 AF XY: 0.376 AC XY: 12438 AN XY: 33051

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0121

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.366

Alfa AF: 0.420 Hom.: 32509

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213392; hg19: chrX-101272492;