rs17088439

Variant names:

• chr18-73854856-T-G
• rs17088439

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 0.103 in 152,186 control chromosomes in the GnomAD database, including 1,122 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 0.10 (1122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.103 AC: 15658 AN: 152068 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.103 AC: 15681 AN: 152186 Hom.: 1122 Cov.: 32 AF XY: 0.104 AC XY: 7727 AN XY: 74420

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.0624 Hom.: 406

Bravo AF: 0.113

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17088439; hg19: chr18-71522091;