9-116409768-A-G

Variant names:

• chr9-116409768-A-G
• rs17302884

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 0.372 in 151,756 control chromosomes in the GnomAD database, including 10,911 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 0.37 (10911 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59

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 (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.372 AC: 56422 AN: 151638 Hom.: 10904 Cov.: 30

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.372 AC: 56456 AN: 151756 Hom.: 10911 Cov.: 30 AF XY: 0.366 AC XY: 27163 AN XY: 74128

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.376

Alfa AF: 0.392 Hom.: 21932

Bravo AF: 0.360

Asia WGS AF: 0.169 AC: 591 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	14
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17302884; hg19: chr9-119172047;