chr13-27811620-C-T

Variant names:

• chr13-27811620-C-T
• rs9512879

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 0.842 in 152,126 control chromosomes in the GnomAD database, including 54,496 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 0.84 (54496 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.842 AC: 128058 AN: 152008 Hom.: 54450 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.842 AC: 128158 AN: 152126 Hom.: 54496 Cov.: 31 AF XY: 0.836 AC XY: 62189 AN XY: 74380

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.818

Alfa AF: 0.821 Hom.: 27180

Bravo AF: 0.856

Asia WGS AF: 0.641 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9512879; hg19: chr13-28385757;