X-140156297-C-T

Variant names:

• chrX-140156297-C-T
• rs613278

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 0.47 in 109,686 control chromosomes in the GnomAD database, including 8,852 homozygotes. There are 14,977 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 0.47 (8852 hom., 14977 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.470 AC: 51529 AN: 109638 Hom.: 8845 Cov.: 22 AF XY: 0.468 AC XY: 14959 AN XY: 31966

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.470 AC: 51549 AN: 109686 Hom.: 8852 Cov.: 22 AF XY: 0.468 AC XY: 14977 AN XY: 32024

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.473

Alfa AF: 0.491 Hom.: 3946

Bravo AF: 0.466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs613278; hg19: chrX-139238459;