rs4131175

Variant names:

• chrX-25461786-C-T
• rs4131175

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 0.558 in 111,054 control chromosomes in the GnomAD database, including 13,988 homozygotes. There are 18,572 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 0.56 (13988 hom., 18572 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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: 0.558 AC: 61919 AN: 111001 Hom.: 13990 Cov.: 23 AF XY: 0.557 AC XY: 18517 AN XY: 33233

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.558 AC: 61970 AN: 111054 Hom.: 13988 Cov.: 23 AF XY: 0.558 AC XY: 18572 AN XY: 33296

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.541

Alfa AF: 0.453 Hom.: 4281

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131175; hg19: chrX-25479903;