13-85596379-A-C

Variant names:

• chr13-85596379-A-C
• rs619982

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.863 in 152,104 control chromosomes in the GnomAD database, including 58,868 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 0.86 (58868 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131139 AN: 151986 Hom.: 58845 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.863 AC: 131206 AN: 152104 Hom.: 58868 Cov.: 31 AF XY: 0.867 AC XY: 64439 AN XY: 74336

African (AFR) AF: 0.582 AC: 24136 AN: 41448

American (AMR) AF: 0.934 AC: 14272 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3392 AN: 3472

East Asian (EAS) AF: 0.980 AC: 5036 AN: 5140

South Asian (SAS) AF: 0.916 AC: 4416 AN: 4822

European-Finnish (FIN) AF: 0.993 AC: 10532 AN: 10604

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66378 AN: 68018

Other (OTH) AF: 0.884 AC: 1868 AN: 2112

Alfa AF: 0.898 Hom.: 8165

Bravo AF: 0.848

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.6
DANN	Benign	0.74
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs619982; hg19: chr13-86170514;