rs6051366

Variant names:

• chr20-2763792-C-T
• rs6051366

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;