20-51865839-T-C

Variant names:

• chr20-51865839-T-C
• rs6063725

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 0.316 in 152,128 control chromosomes in the GnomAD database, including 9,246 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 0.32 (9246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48092 AN: 152010 Hom.: 9247 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.316 AC: 48087 AN: 152128 Hom.: 9246 Cov.: 32 AF XY: 0.317 AC XY: 23538 AN XY: 74360

African (AFR) AF: 0.0931 AC: 3868 AN: 41548

American (AMR) AF: 0.380 AC: 5806 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1543 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2156 AN: 5150

South Asian (SAS) AF: 0.430 AC: 2078 AN: 4828

European-Finnish (FIN) AF: 0.384 AC: 4063 AN: 10580

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27415 AN: 67974

Other (OTH) AF: 0.356 AC: 753 AN: 2114

Alfa AF: 0.379 Hom.: 34606

Bravo AF: 0.306

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs6063725; hg19: chr20-50482378;