rs17790217

chr18-68126082-T-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 0.446 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.446 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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.462

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17790217; hg19: chr18-65793319;