rs17150478

Variant names:

• chr8-9783524-A-G
• rs17150478

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 0.147 in 152,174 control chromosomes in the GnomAD database, including 2,133 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 0.15 (2133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.147 AC: 22304 AN: 152054 Hom.: 2134 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.147 AC: 22306 AN: 152174 Hom.: 2133 Cov.: 32 AF XY: 0.150 AC XY: 11192 AN XY: 74376

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0783

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.132

Alfa AF: 0.168 Hom.: 1599

Bravo AF: 0.135

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.010
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17150478; hg19: chr8-9641034;