chr13-86540492-C-T

Variant names:

• chr13-86540492-C-T
• rs9301538

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 0.645 in 151,616 control chromosomes in the GnomAD database, including 31,956 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 0.64 (31956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.645 AC: 97643 AN: 151498 Hom.: 31917 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.645 AC: 97740 AN: 151616 Hom.: 31956 Cov.: 32 AF XY: 0.641 AC XY: 47505 AN XY: 74056

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.627

Alfa AF: 0.607 Hom.: 11352

Bravo AF: 0.653

Asia WGS AF: 0.604 AC: 2098 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9301538; hg19: chr13-87192747;