rs6051366

Variant names:

• chr20-2763792-C-T
• rs6051366

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 0.272 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
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.272 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

African (AFR) AF: 0.353 AC: 14624 AN: 41458

American (AMR) AF: 0.244 AC: 3725 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1748 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1064 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16445 AN: 67990

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.243 Hom.: 5731

Bravo AF: 0.276

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6051366; hg19: chr20-2744438;