chr9-130658892-G-A

Variant names:

• chr9-130658892-G-A
• rs3802344

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 0.0607 in 152,138 control chromosomes in the GnomAD database, including 327 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 0.061 (327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.102 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: 0.0605 AC: 9204 AN: 152020 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0607 AC: 9228 AN: 152138 Hom.: 327 Cov.: 32 AF XY: 0.0612 AC XY: 4554 AN XY: 74388

African (AFR) AF: 0.0489 AC: 2029 AN: 41510

American (AMR) AF: 0.0829 AC: 1268 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5162

South Asian (SAS) AF: 0.110 AC: 528 AN: 4812

European-Finnish (FIN) AF: 0.0492 AC: 522 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4391 AN: 67956

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0628 Hom.: 251

Bravo AF: 0.0607

Asia WGS AF: 0.0710 AC: 246 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	3.6
DANN	Benign	0.54
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs3802344; hg19: chr9-133534279;