13-83219840-C-T

Variant names:

• chr13-83219840-C-T
• rs2669264

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 0.838 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.828

Alfa AF: 0.869 Hom.: 99850

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2669264; hg19: chr13-83793975;