rs17658378

Variant names:

• chr8-115381846-A-G
• rs17658378

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 0.0824 in 152,174 control chromosomes in the GnomAD database, including 759 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 0.082 (759 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.122 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: 0.0825 AC: 12541 AN: 152056 Hom.: 760 Cov.: 31

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0824 AC: 12540 AN: 152174 Hom.: 759 Cov.: 31 AF XY: 0.0788 AC XY: 5859 AN XY: 74392

Gnomad4 AFR AF: 0.0243

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.116

Alfa AF: 0.115 Hom.: 1989

Bravo AF: 0.0878

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
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: rs17658378; hg19: chr8-116394075;