rs619982

Positions:

• chr13-85596379-A-C
• chr13-85596379-A-G
• chr13-85596379-A-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 0.863 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.863 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

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.884

Alfa AF: 0.911 Hom.: 8030

Bravo AF: 0.848

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs619982; hg19: chr13-86170514;