9-80640399-G-A

Variant names:

• chr9-80640399-G-A
• rs2183004

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 0.295 in 151,408 control chromosomes in the GnomAD database, including 7,021 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 0.29 (7021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44583 AN: 151292 Hom.: 7011 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.295 AC: 44613 AN: 151408 Hom.: 7021 Cov.: 31 AF XY: 0.303 AC XY: 22436 AN XY: 73936

African (AFR) AF: 0.224 AC: 9264 AN: 41280

American (AMR) AF: 0.359 AC: 5449 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2676 AN: 5106

South Asian (SAS) AF: 0.514 AC: 2463 AN: 4792

European-Finnish (FIN) AF: 0.374 AC: 3918 AN: 10470

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18884 AN: 67818

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.289 Hom.: 7179

Bravo AF: 0.288

Asia WGS AF: 0.484 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.56
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2183004; hg19: chr9-83255314;