chr18-68126082-T-A

Variant names:

• chr18-68126082-T-A
• rs17790217

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;