rs17088339

Variant names:

• chr18-73808898-T-A
• rs17088339

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 0.0863 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0240 AC: 996 AN: 41548

American (AMR) AF: 0.195 AC: 2980 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.173 AC: 893 AN: 5172

South Asian (SAS) AF: 0.0625 AC: 302 AN: 4830

European-Finnish (FIN) AF: 0.0846 AC: 898 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6479 AN: 68010

Other (OTH) AF: 0.0855 AC: 181 AN: 2116

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs17088339; hg19: chr18-71476133;