chrX-145456762-C-T

Variant names:

• chrX-145456762-C-T
• rs1174067

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 0.33 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.105 AC: 3205 AN: 30551

American (AMR) AF: 0.410 AC: 4210 AN: 10266

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 981 AN: 2631

East Asian (EAS) AF: 0.288 AC: 1009 AN: 3501

South Asian (SAS) AF: 0.457 AC: 1184 AN: 2591

European-Finnish (FIN) AF: 0.406 AC: 2321 AN: 5715

Middle Eastern (MID) AF: 0.524 AC: 110 AN: 210

European-Non Finnish (NFE) AF: 0.428 AC: 22552 AN: 52643

Other (OTH) AF: 0.369 AC: 552 AN: 1496

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1174067; hg19: chrX-144538280;