rs9538394

chr13-59354287-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 0.38 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.380 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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.416

Alfa AF: 0.401 Hom.: 11934

Bravo AF: 0.389

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

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