rs17517421

Variant names:

• chr8-18508305-G-A
• rs17517421

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 0.127 in 152,204 control chromosomes in the GnomAD database, including 1,316 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 0.13 (1316 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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: 0.127 AC: 19256 AN: 152086 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19275 AN: 152204 Hom.: 1316 Cov.: 33 AF XY: 0.127 AC XY: 9420 AN XY: 74398

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0978

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.0800

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.117

Alfa AF: 0.118 Hom.: 189

Bravo AF: 0.128

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17517421; hg19: chr8-18365815;