rs203491

Variant names:

• chrX-127183695-T-A
• rs203491

Your query was ambiguous. Multiple possible variants found:

• chrX-127183695-T-A
• chrX-127183695-T-C
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;