20-46139085-T-A

Position:

• chr20-46139085-T-A

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 0.364 in 152,100 control chromosomes in the GnomAD database, including 11,807 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 0.36 (11807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.364 AC: 55280 AN: 151982 Hom.: 11805 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.364 AC: 55297 AN: 152100 Hom.: 11807 Cov.: 32 AF XY: 0.366 AC XY: 27229 AN XY: 74322

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.377

Alfa AF: 0.394 Hom.: 1684

Bravo AF: 0.359

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535043; hg19: chr20-44767724;