chr13-59354287-G-T

Variant names:

• chr13-59354287-G-T
• rs9538394

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 0.38 in 151,924 control chromosomes in the GnomAD database, including 11,798 homozygotes. 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 0.38 (11798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.380 AC: 57682 AN: 151806 Hom.: 11785 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.380 AC: 57726 AN: 151924 Hom.: 11798 Cov.: 31 AF XY: 0.385 AC XY: 28556 AN XY: 74254

African (AFR) AF: 0.246 AC: 10196 AN: 41428

American (AMR) AF: 0.506 AC: 7723 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3614 AN: 5152

South Asian (SAS) AF: 0.546 AC: 2633 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3757 AN: 10558

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26982 AN: 67928

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.397 Hom.: 15513

Bravo AF: 0.389

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs9538394; hg19: chr13-59928421; COSMIC: COSV69355158;