chrX-148363936-G-T

Variant names:

• chrX-148363936-G-T
• rs2159768

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 0.47 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
• Publications: 0 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 52066 AN: 110671 Hom.: 9952 Cov.: 23

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

African (AFR) AF: 0.188 AC: 5748 AN: 30651

American (AMR) AF: 0.677 AC: 7008 AN: 10357

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1146 AN: 2631

East Asian (EAS) AF: 0.854 AC: 2952 AN: 3457

South Asian (SAS) AF: 0.462 AC: 1215 AN: 2632

European-Finnish (FIN) AF: 0.633 AC: 3682 AN: 5815

Middle Eastern (MID) AF: 0.481 AC: 103 AN: 214

European-Non Finnish (NFE) AF: 0.548 AC: 28948 AN: 52785

Other (OTH) AF: 0.485 AC: 735 AN: 1514

Alfa AF: 0.509 Hom.: 3782

Bravo AF: 0.471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.57
DANN	Benign	0.36
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2159768; hg19: chrX-147445456;