20-252982-A-T

Variant names:

• chr20-252982-A-T
• rs1774116

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 0.365 in 152,060 control chromosomes in the GnomAD database, including 11,404 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 0.36 (11404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55434 AN: 151942 Hom.: 11390 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.365 AC: 55467 AN: 152060 Hom.: 11404 Cov.: 32 AF XY: 0.366 AC XY: 27222 AN XY: 74294

African (AFR) AF: 0.168 AC: 6980 AN: 41490

American (AMR) AF: 0.366 AC: 5591 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2533 AN: 5146

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4818

European-Finnish (FIN) AF: 0.475 AC: 5013 AN: 10560

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30591 AN: 67980

Other (OTH) AF: 0.424 AC: 893 AN: 2108

Alfa AF: 0.391 Hom.: 1535

Bravo AF: 0.353

Asia WGS AF: 0.451 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1774116; hg19: chr20-233623;