chr9-108673352-A-G

Variant names:

• chr9-108673352-A-G
• rs11794727

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 0.0596 in 152,338 control chromosomes in the GnomAD database, including 347 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 0.060 (347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9067 AN: 152220 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0368

Gnomad FIN AF: 0.0429

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0596 AC: 9073 AN: 152338 Hom.: 347 Cov.: 32 AF XY: 0.0577 AC XY: 4296 AN XY: 74496

African (AFR) AF: 0.0275 AC: 1145 AN: 41588

American (AMR) AF: 0.0763 AC: 1168 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3472

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5188

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4830

European-Finnish (FIN) AF: 0.0429 AC: 455 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5685 AN: 68024

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0773 Hom.: 871

Bravo AF: 0.0601

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs11794727; hg19: chr9-111435632;