chr20-18097908-G-A

Variant names:

• chr20-18097908-G-A
• rs1124933

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 0.437 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.362 AC: 14948 AN: 41324

American (AMR) AF: 0.528 AC: 8040 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4676 AN: 5152

South Asian (SAS) AF: 0.631 AC: 3036 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4441 AN: 10512

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28507 AN: 67938

Other (OTH) AF: 0.440 AC: 924 AN: 2102

Alfa AF: 0.430 Hom.: 24856

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1124933; hg19: chr20-18078552;