X-148363936-G-T

Position:

• chrX-148363936-G-T

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 110,723 control chromosomes in the GnomAD database, including 9,960 homozygotes. There are 15,784 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 (9960 hom., 15784 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 52066 AN: 110671 Hom.: 9952 Cov.: 23 AF XY: 0.479 AC XY: 15784 AN XY: 32933

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.489

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.470 AC: 52067 AN: 110723 Hom.: 9960 Cov.: 23 AF XY: 0.478 AC XY: 15784 AN XY: 32995

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.485

Alfa AF: 0.509 Hom.: 3782

Bravo AF: 0.471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.57
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2159768; hg19: chrX-147445456;