rs2065982

Variant names:

• chr13-34290103-T-C
• rs2065982

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 0.118 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0881 AC: 3658 AN: 41516

American (AMR) AF: 0.314 AC: 4790 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3662 AN: 5138

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4818

European-Finnish (FIN) AF: 0.0642 AC: 681 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0495 AC: 3368 AN: 68004

Other (OTH) AF: 0.130 AC: 273 AN: 2100

Alfa AF: 0.0776 Hom.: 154

Bravo AF: 0.143

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.50
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2065982; hg19: chr13-34864240;