rs2213392

Variant names:

• chrX-102017519-G-T
• rs2213392

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;