X-25717771-C-T

Variant names:

• chrX-25717771-C-T
• rs1025952

Variant summary

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

The variant allele was found at a frequency of 0.436 in 110,134 control chromosomes in the GnomAD database, including 7,714 homozygotes. There are 14,079 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 0.44 (7714 hom., 14079 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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: 0.436 AC: 47967 AN: 110080 Hom.: 7715 Cov.: 22

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 47987 AN: 110134 Hom.: 7714 Cov.: 22 AF XY: 0.434 AC XY: 14079 AN XY: 32472

African (AFR) AF: 0.533 AC: 16144 AN: 30265

American (AMR) AF: 0.461 AC: 4769 AN: 10353

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1067 AN: 2622

East Asian (EAS) AF: 0.629 AC: 2161 AN: 3437

South Asian (SAS) AF: 0.419 AC: 1091 AN: 2605

European-Finnish (FIN) AF: 0.451 AC: 2626 AN: 5824

Middle Eastern (MID) AF: 0.300 AC: 64 AN: 213

European-Non Finnish (NFE) AF: 0.368 AC: 19358 AN: 52645

Other (OTH) AF: 0.431 AC: 642 AN: 1489

Alfa AF: 0.401 Hom.: 29946

Bravo AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.53
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1025952; hg19: chrX-25735888;