chr20-46739515-T-C

Variant names:

• chr20-46739515-T-C
• rs6066059

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 0.248 in 151,994 control chromosomes in the GnomAD database, including 5,629 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 0.25 (5629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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: 0.249 AC: 37762 AN: 151876 Hom.: 5627 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.248 AC: 37768 AN: 151994 Hom.: 5629 Cov.: 31 AF XY: 0.253 AC XY: 18784 AN XY: 74282

African (AFR) AF: 0.100 AC: 4162 AN: 41500

American (AMR) AF: 0.295 AC: 4499 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3034 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4806

European-Finnish (FIN) AF: 0.296 AC: 3124 AN: 10550

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20037 AN: 67930

Other (OTH) AF: 0.279 AC: 587 AN: 2106

Alfa AF: 0.269 Hom.: 7454

Bravo AF: 0.243

Asia WGS AF: 0.375 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.82
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6066059; hg19: chr20-45368154;