20-2763792-C-T

Position:

• chr20-2763792-C-T

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 0.272 in 152,080 control chromosomes in the GnomAD database, including 5,937 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 0.27 (5937 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41366 AN: 151960 Hom.: 5919 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.272 AC: 41431 AN: 152080 Hom.: 5937 Cov.: 32 AF XY: 0.271 AC XY: 20145 AN XY: 74352

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.250

Alfa AF: 0.238 Hom.: 4157

Bravo AF: 0.276

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6051366; hg19: chr20-2744438;