20-53527724-G-A

Variant names:

• chr20-53527724-G-A
• rs2766648

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 0.437 in 152,002 control chromosomes in the GnomAD database, including 14,751 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 0.44 (14751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66422 AN: 151884 Hom.: 14748 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.437 AC: 66443 AN: 152002 Hom.: 14751 Cov.: 32 AF XY: 0.436 AC XY: 32384 AN XY: 74302

African (AFR) AF: 0.380 AC: 15739 AN: 41470

American (AMR) AF: 0.427 AC: 6528 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5148

South Asian (SAS) AF: 0.393 AC: 1894 AN: 4816

European-Finnish (FIN) AF: 0.520 AC: 5485 AN: 10554

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31681 AN: 67960

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.451 Hom.: 7614

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.58
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2766648; hg19: chr20-52144263;