chr9-117674839-G-A

Variant names:

• chr9-117674839-G-A
• rs1329061

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 0.528 in 151,794 control chromosomes in the GnomAD database, including 23,795 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 0.53 (23795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.528 AC: 80090 AN: 151676 Hom.: 23802 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.528 AC: 80094 AN: 151794 Hom.: 23795 Cov.: 31 AF XY: 0.526 AC XY: 39048 AN XY: 74192

African (AFR) AF: 0.232 AC: 9634 AN: 41442

American (AMR) AF: 0.584 AC: 8881 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2137 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3163 AN: 5108

South Asian (SAS) AF: 0.618 AC: 2981 AN: 4820

European-Finnish (FIN) AF: 0.554 AC: 5857 AN: 10568

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45359 AN: 67890

Other (OTH) AF: 0.570 AC: 1195 AN: 2098

Alfa AF: 0.589 Hom.: 4755

Bravo AF: 0.520

Asia WGS AF: 0.590 AC: 2051 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1329061; hg19: chr9-120437117;