20-46833786-T-C

Variant names:

• chr20-46833786-T-C
• rs6066085

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 0.529 in 152,064 control chromosomes in the GnomAD database, including 23,166 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 0.53 (23166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 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: 0.529 AC: 80345 AN: 151946 Hom.: 23160 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.529 AC: 80375 AN: 152064 Hom.: 23166 Cov.: 32 AF XY: 0.521 AC XY: 38698 AN XY: 74338

African (AFR) AF: 0.367 AC: 15227 AN: 41472

American (AMR) AF: 0.463 AC: 7066 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3468

East Asian (EAS) AF: 0.0882 AC: 458 AN: 5190

South Asian (SAS) AF: 0.366 AC: 1768 AN: 4828

European-Finnish (FIN) AF: 0.645 AC: 6803 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44934 AN: 67976

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

Alfa AF: 0.562 Hom.: 7891

Bravo AF: 0.507

Asia WGS AF: 0.233 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.42
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6066085; hg19: chr20-45462425;