2-20445745-C-T

Variant names:

• chr2-20445745-C-T
• rs2602160

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 0.764 in 151,980 control chromosomes in the GnomAD database, including 44,605 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 0.76 (44605 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 4 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 = 0.895 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: 0.764 AC: 116060 AN: 151862 Hom.: 44549 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.764 AC: 116177 AN: 151980 Hom.: 44605 Cov.: 30 AF XY: 0.769 AC XY: 57155 AN XY: 74284

African (AFR) AF: 0.797 AC: 33033 AN: 41464

American (AMR) AF: 0.816 AC: 12471 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2406 AN: 3468

East Asian (EAS) AF: 0.917 AC: 4713 AN: 5140

South Asian (SAS) AF: 0.811 AC: 3905 AN: 4814

European-Finnish (FIN) AF: 0.750 AC: 7913 AN: 10548

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49324 AN: 67942

Other (OTH) AF: 0.767 AC: 1616 AN: 2108

Alfa AF: 0.742 Hom.: 20184

Bravo AF: 0.770

Asia WGS AF: 0.861 AC: 2993 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	0.55
DANN	Benign	0.50
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2602160; hg19: chr2-20645506;