rs17517421

chr8-18508305-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;