chr20-46134645-C-T

Variant names:

• chr20-46134645-C-T
• rs4813003

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 0.189 in 152,200 control chromosomes in the GnomAD database, including 3,062 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 0.19 (3062 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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: 0.189 AC: 28720 AN: 152082 Hom.: 3061 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.189 AC: 28753 AN: 152200 Hom.: 3062 Cov.: 31 AF XY: 0.194 AC XY: 14419 AN XY: 74414

African (AFR) AF: 0.217 AC: 9005 AN: 41524

American (AMR) AF: 0.283 AC: 4321 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2198 AN: 5182

South Asian (SAS) AF: 0.186 AC: 898 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1609 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9626 AN: 68002

Other (OTH) AF: 0.183 AC: 387 AN: 2116

Alfa AF: 0.161 Hom.: 7636

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4813003; hg19: chr20-44763284;