20-46148866-G-T

Variant names:

• chr20-46148866-G-T
• rs2064405

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 0.0794 in 152,206 control chromosomes in the GnomAD database, including 593 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 0.079 (593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0794 AC: 12080 AN: 152088 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0784

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0794 AC: 12084 AN: 152206 Hom.: 593 Cov.: 32 AF XY: 0.0811 AC XY: 6033 AN XY: 74394

African (AFR) AF: 0.0336 AC: 1395 AN: 41528

American (AMR) AF: 0.0782 AC: 1196 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0930 AC: 448 AN: 4816

European-Finnish (FIN) AF: 0.122 AC: 1291 AN: 10586

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7157 AN: 68016

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0837 Hom.: 970

Bravo AF: 0.0719

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2064405; hg19: chr20-44777505;