20-46134645-C-T

Position:

• chr20-46134645-C-T

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.183

Alfa AF: 0.156 Hom.: 2995

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4813003; hg19: chr20-44763284;