20-18905094-G-A

Variant names:

• chr20-18905094-G-A
• rs742731

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 0.418 in 152,062 control chromosomes in the GnomAD database, including 13,552 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 0.42 (13552 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63541 AN: 151944 Hom.: 13516 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.418 AC: 63633 AN: 152062 Hom.: 13552 Cov.: 33 AF XY: 0.417 AC XY: 30976 AN XY: 74330

African (AFR) AF: 0.496 AC: 20545 AN: 41458

American (AMR) AF: 0.462 AC: 7059 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1330 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1490 AN: 5182

South Asian (SAS) AF: 0.449 AC: 2161 AN: 4818

European-Finnish (FIN) AF: 0.336 AC: 3552 AN: 10562

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26152 AN: 67994

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.409 Hom.: 17891

Bravo AF: 0.430

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.5
DANN	Benign	0.58
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs742731; hg19: chr20-18885738;