rs17088339

Variant names:

• chr18-73808898-T-A
• rs17088339

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 0.0863 in 152,246 control chromosomes in the GnomAD database, including 830 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 0.086 (830 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 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: 0.0863 AC: 13133 AN: 152128 Hom.: 828 Cov.: 33

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0863 AC: 13138 AN: 152246 Hom.: 830 Cov.: 33 AF XY: 0.0891 AC XY: 6634 AN XY: 74424

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.0625

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0833 Hom.: 103

Bravo AF: 0.0952

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17088339; hg19: chr18-71476133;