13-80094739-T-C

Position:

• chr13-80094739-T-C

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 0.653 in 151,994 control chromosomes in the GnomAD database, including 34,133 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 0.65 (34133 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.653 AC: 99150 AN: 151876 Hom.: 34131 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.653 AC: 99188 AN: 151994 Hom.: 34133 Cov.: 31 AF XY: 0.650 AC XY: 48316 AN XY: 74286

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.693

Alfa AF: 0.734 Hom.: 64195

Bravo AF: 0.656

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9574565; hg19: chr13-80668874;