chr20-599013-A-G

Variant names:

• chr20-599013-A-G
• rs282152

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.914 AC: 37894 AN: 41478

American (AMR) AF: 0.673 AC: 10277 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2414 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5156 AN: 5180

South Asian (SAS) AF: 0.767 AC: 3684 AN: 4806

European-Finnish (FIN) AF: 0.650 AC: 6867 AN: 10566

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43919 AN: 67948

Other (OTH) AF: 0.735 AC: 1550 AN: 2110

Alfa AF: 0.681 Hom.: 33671

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs282152; hg19: chr20-579657;