20-46107215-A-G

Position:

• chr20-46107215-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.816 in 152,214 control chromosomes in the GnomAD database, including 51,358 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 0.82 (51358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.816 AC: 124035 AN: 152096 Hom.: 51294 Cov.: 32

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.816 AC: 124157 AN: 152214 Hom.: 51358 Cov.: 32 AF XY: 0.813 AC XY: 60532 AN XY: 74416

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.788

Alfa AF: 0.787 Hom.: 8035

Bravo AF: 0.830

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	17
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6065926; hg19: chr20-44735854;