rs9538394

Variant names:

• chr13-59354287-G-T
• rs9538394

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;