13-79594869-C-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 0.539 in 151,832 control chromosomes in the GnomAD database, including 22,639 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 0.54 (22639 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.538 AC: 81681 AN: 151714 Hom.: 22598 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.539 AC: 81787 AN: 151832 Hom.: 22639 Cov.: 31 AF XY: 0.536 AC XY: 39798 AN XY: 74214

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.545

Alfa AF: 0.497 Hom.: 31366

Bravo AF: 0.556

Asia WGS AF: 0.432 AC: 1505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.29
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9601248; hg19: chr13-80169004;