20-18097908-G-A

Position:

• chr20-18097908-G-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 0.437 in 151,744 control chromosomes in the GnomAD database, including 15,413 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 0.44 (15413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.437 AC: 66291 AN: 151626 Hom.: 15401 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.437 AC: 66340 AN: 151744 Hom.: 15413 Cov.: 31 AF XY: 0.446 AC XY: 33033 AN XY: 74138

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.440

Alfa AF: 0.430 Hom.: 19732

Bravo AF: 0.443

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1124933; hg19: chr20-18078552;