rs2065982

Variant names:

• chr13-34290103-T-C
• rs2065982

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 0.118 in 152,110 control chromosomes in the GnomAD database, including 2,659 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 0.12 (2659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

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 (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.118 AC: 17962 AN: 151992 Hom.: 2654 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.118 AC: 17982 AN: 152110 Hom.: 2659 Cov.: 32 AF XY: 0.128 AC XY: 9552 AN XY: 74350

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0642

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0769 Hom.: 153

Bravo AF: 0.143

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2065982; hg19: chr13-34864240;