20-252982-A-T

Variant names:

• chr20-252982-A-T
• rs1774116

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 0.365 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.424

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1774116; hg19: chr20-233623;