13-83219840-C-T

Variant names:

• chr13-83219840-C-T
• rs2669264

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 0.838 in 151,636 control chromosomes in the GnomAD database, including 53,414 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 0.84 (53414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.889 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: 0.838 AC: 126962 AN: 151518 Hom.: 53378 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.838 AC: 127052 AN: 151636 Hom.: 53414 Cov.: 33 AF XY: 0.837 AC XY: 62053 AN XY: 74114

African (AFR) AF: 0.773 AC: 32060 AN: 41452

American (AMR) AF: 0.823 AC: 12485 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2846 AN: 3460

East Asian (EAS) AF: 0.746 AC: 3818 AN: 5118

South Asian (SAS) AF: 0.911 AC: 4386 AN: 4814

European-Finnish (FIN) AF: 0.862 AC: 9134 AN: 10596

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59602 AN: 67722

Other (OTH) AF: 0.828 AC: 1738 AN: 2100

Alfa AF: 0.864 Hom.: 151744

Bravo AF: 0.832

Asia WGS AF: 0.828 AC: 2877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2669264; hg19: chr13-83793975;