rs1344063

chr2-20961673-T-Cchr2-20961673-T-G

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 0.546 in 152,162 control chromosomes in the GnomAD database, including 23,256 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 0.55 (23256 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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 = 0.836 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: 0.546 AC: 83019 AN: 152042 Hom.: 23253 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.546 AC: 83049 AN: 152162 Hom.: 23256 Cov.: 33 AF XY: 0.548 AC XY: 40720 AN XY: 74374

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.564

Alfa AF: 0.576 Hom.: 37346

Bravo AF: 0.537

Asia WGS AF: 0.749 AC: 2603 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	0.084
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344063; hg19: chr2-21184545;