rs4131175

Positions:

• chrX-25461786-C-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 0.558 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.25461786C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;