20-46111557-C-T

Variant names:

• chr20-46111557-C-T
• rs6074022

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.769

Alfa AF: 0.743 Hom.: 88133

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

Splicing

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

Publications

LitVar

Other links and lift over

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