rs17790217

Variant names:

• chr18-68126082-T-A
• rs17790217

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 0.446 in 152,034 control chromosomes in the GnomAD database, including 15,757 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 0.45 (15757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67697 AN: 151916 Hom.: 15743 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.446 AC: 67742 AN: 152034 Hom.: 15757 Cov.: 32 AF XY: 0.441 AC XY: 32791 AN XY: 74332

African (AFR) AF: 0.382 AC: 15834 AN: 41444

American (AMR) AF: 0.359 AC: 5491 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5168

South Asian (SAS) AF: 0.313 AC: 1513 AN: 4830

European-Finnish (FIN) AF: 0.573 AC: 6058 AN: 10572

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34424 AN: 67956

Other (OTH) AF: 0.462 AC: 976 AN: 2114

Alfa AF: 0.490 Hom.: 2284

Bravo AF: 0.426

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs17790217; hg19: chr18-65793319;