2-20961673-T-C

Variant names:

• chr2-20961673-T-C
• rs1344063

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 0.546 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
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 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: 0.546 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

African (AFR) AF: 0.450 AC: 18675 AN: 41506

American (AMR) AF: 0.489 AC: 7480 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4431 AN: 5168

South Asian (SAS) AF: 0.727 AC: 3511 AN: 4828

European-Finnish (FIN) AF: 0.535 AC: 5671 AN: 10594

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39080 AN: 68000

Other (OTH) AF: 0.564 AC: 1191 AN: 2110

Alfa AF: 0.568 Hom.: 87495

Bravo AF: 0.537

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.084
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1344063; hg19: chr2-21184545;