rs2097402

chrX-134983524-G-AchrX-134983524-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 0.366 in 111,089 control chromosomes in the GnomAD database, including 5,722 homozygotes. There are 11,793 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 0.37 (5722 hom., 11793 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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: 0.366 AC: 40678 AN: 111034 Hom.: 5720 Cov.: 23 AF XY: 0.354 AC XY: 11767 AN XY: 33260

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.366 AC: 40694 AN: 111089 Hom.: 5722 Cov.: 23 AF XY: 0.354 AC XY: 11793 AN XY: 33325

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.377

Alfa AF: 0.327 Hom.: 27737

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097402; hg19: chrX-134117554;