rs2097402

Variant names:

• chrX-134983524-G-A
• rs2097402

Your query was ambiguous. Multiple possible variants found:

• chrX-134983524-G-A
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;