rs203491

chrX-127183695-T-AchrX-127183695-T-CchrX-127183695-T-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 0.508 in 109,992 control chromosomes in the GnomAD database, including 12,225 homozygotes. There are 16,331 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 0.51 (12225 hom., 16331 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.508 AC: 55832 AN: 109939 Hom.: 12224 Cov.: 22 AF XY: 0.505 AC XY: 16279 AN XY: 32205

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.508 AC: 55880 AN: 109992 Hom.: 12225 Cov.: 22 AF XY: 0.506 AC XY: 16331 AN XY: 32268

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.482

Alfa AF: 0.408 Hom.: 2824

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.83
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs203491; hg19: chrX-126317678;