20-46107215-A-G

Variant names:

• chr20-46107215-A-G
• rs6065926

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;