20-46111557-C-T

Variant names:

• chr20-46111557-C-T
• rs6074022

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 0.793 in 151,100 control chromosomes in the GnomAD database, including 48,259 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 0.79 (48259 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 113 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.793 AC: 119659 AN: 150982 Hom.: 48185 Cov.: 26

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.793 AC: 119794 AN: 151100 Hom.: 48259 Cov.: 26 AF XY: 0.787 AC XY: 58020 AN XY: 73698

African (AFR) AF: 0.942 AC: 38741 AN: 41144

American (AMR) AF: 0.776 AC: 11776 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2826 AN: 5044

South Asian (SAS) AF: 0.738 AC: 3524 AN: 4778

European-Finnish (FIN) AF: 0.721 AC: 7465 AN: 10354

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50410 AN: 67832

Other (OTH) AF: 0.769 AC: 1614 AN: 2100

Alfa AF: 0.757 Hom.: 127224

Bravo AF: 0.804

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6074022; hg19: chr20-44740196; COSMIC: COSV50188835;