20-599013-A-G

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 0.741 in 152,024 control chromosomes in the GnomAD database, including 42,998 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 0.74 (42998 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112519 AN: 151908 Hom.: 42971 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.741 AC: 112597 AN: 152024 Hom.: 42998 Cov.: 31 AF XY: 0.739 AC XY: 54902 AN XY: 74304

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.735

Alfa AF: 0.672 Hom.: 20302

Bravo AF: 0.752

Asia WGS AF: 0.859 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.51
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282152; hg19: chr20-579657;