chrX-89275066-T-G

Variant names:

• chrX-89275066-T-G
• rs5941160

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 0.401 in 109,245 control chromosomes in the GnomAD database, including 6,997 homozygotes. There are 12,298 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 0.40 (6997 hom., 12298 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.401 AC: 43779 AN: 109189 Hom.: 7000 Cov.: 21

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 43780 AN: 109245 Hom.: 6997 Cov.: 21 AF XY: 0.389 AC XY: 12298 AN XY: 31601

African (AFR) AF: 0.226 AC: 6843 AN: 30235

American (AMR) AF: 0.405 AC: 4118 AN: 10156

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1338 AN: 2619

East Asian (EAS) AF: 0.289 AC: 988 AN: 3421

South Asian (SAS) AF: 0.519 AC: 1294 AN: 2493

European-Finnish (FIN) AF: 0.439 AC: 2454 AN: 5590

Middle Eastern (MID) AF: 0.467 AC: 99 AN: 212

European-Non Finnish (NFE) AF: 0.491 AC: 25690 AN: 52362

Other (OTH) AF: 0.432 AC: 643 AN: 1488

Alfa AF: 0.440 Hom.: 3456

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs5941160; hg19: chrX-88530065;