rs17040318

Variant names:

• chr9-135573469-A-G
• rs17040318

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 0.0589 in 152,130 control chromosomes in the GnomAD database, including 775 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 0.059 (775 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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: 0.0587 AC: 8930 AN: 152014 Hom.: 769 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00406

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00221

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0589 AC: 8964 AN: 152130 Hom.: 775 Cov.: 33 AF XY: 0.0579 AC XY: 4308 AN XY: 74380

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0211

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0883

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.00406

Gnomad4 NFE AF: 0.00221

Gnomad4 OTH AF: 0.0465

Alfa AF: 0.0263 Hom.: 52

Bravo AF: 0.0660

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
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: rs17040318; hg19: chr9-138465315;