chr20-46000651-T-A

Variant names:

• chr20-46000651-T-A
• rs6094237

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.562 in 152,006 control chromosomes in the GnomAD database, including 24,488 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 0.56 (24488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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: 0.562 AC: 85380 AN: 151888 Hom.: 24491 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.562 AC: 85405 AN: 152006 Hom.: 24488 Cov.: 33 AF XY: 0.554 AC XY: 41150 AN XY: 74286

African (AFR) AF: 0.566 AC: 23449 AN: 41440

American (AMR) AF: 0.560 AC: 8551 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1249 AN: 5162

South Asian (SAS) AF: 0.441 AC: 2118 AN: 4808

European-Finnish (FIN) AF: 0.510 AC: 5394 AN: 10570

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40705 AN: 67960

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.559 Hom.: 2879

Bravo AF: 0.562

Asia WGS AF: 0.331 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.89
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6094237; hg19: chr20-44629290;