rs4131175

Variant names:

• chrX-25461786-C-T
• rs4131175
• ENST00000723704.1:n.357-10169C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000723704.1(ENSG00000294456):​n.357-10169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000294456 ENST00000723704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

Genes affected

ENSG00000294456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294456	ENST00000723704.1	n.357-10169C>T		intron_variant	Intron 3 of 5
ENSG00000294456	ENST00000723705.1	n.408-10169C>T		intron_variant	Intron 4 of 6
ENSG00000294456	ENST00000723706.1	n.350-10169C>T		intron_variant	Intron 4 of 6
ENSG00000294456	ENST00000723707.1	n.283-10169C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 61919 AN: 111001 Hom.: 13990 Cov.: 23

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

African (AFR) AF: 0.882 AC: 26957 AN: 30568

American (AMR) AF: 0.579 AC: 6061 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 985 AN: 2639

East Asian (EAS) AF: 0.587 AC: 2043 AN: 3479

South Asian (SAS) AF: 0.699 AC: 1865 AN: 2668

European-Finnish (FIN) AF: 0.427 AC: 2522 AN: 5900

Middle Eastern (MID) AF: 0.507 AC: 108 AN: 213

European-Non Finnish (NFE) AF: 0.387 AC: 20473 AN: 52915

Other (OTH) AF: 0.541 AC: 825 AN: 1524

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4131175; hg19: chrX-25479903;