X-145456762-C-T

Variant names:

• chrX-145456762-C-T
• rs1174067

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 0.33 in 110,283 control chromosomes in the GnomAD database, including 5,186 homozygotes. There are 10,765 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 0.33 (5186 hom., 10765 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.330 AC: 36408 AN: 110227 Hom.: 5185 Cov.: 22 AF XY: 0.331 AC XY: 10755 AN XY: 32493

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.330 AC: 36413 AN: 110283 Hom.: 5186 Cov.: 22 AF XY: 0.331 AC XY: 10765 AN XY: 32559

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.369

Alfa AF: 0.205 Hom.: 1172

Bravo AF: 0.317

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1174067; hg19: chrX-144538280;