9-116409768-A-G

Variant names:

• chr9-116409768-A-G
• rs17302884

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.365 AC: 15095 AN: 41378

American (AMR) AF: 0.295 AC: 4490 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3472

East Asian (EAS) AF: 0.118 AC: 606 AN: 5146

South Asian (SAS) AF: 0.235 AC: 1126 AN: 4796

European-Finnish (FIN) AF: 0.430 AC: 4517 AN: 10500

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28045 AN: 67910

Other (OTH) AF: 0.376 AC: 792 AN: 2106

Alfa AF: 0.388 Hom.: 34349

Bravo AF: 0.360

Asia WGS AF: 0.169 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.28
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs17302884; hg19: chr9-119172047;