chr9-12531726-C-G

Variant names:

• chr9-12531726-C-G
• rs1408806

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 0.275 in 151,970 control chromosomes in the GnomAD database, including 7,508 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 0.27 (7508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.275 AC: 41721 AN: 151852 Hom.: 7503 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.275 AC: 41724 AN: 151970 Hom.: 7508 Cov.: 31 AF XY: 0.288 AC XY: 21420 AN XY: 74254

African (AFR) AF: 0.166 AC: 6872 AN: 41478

American (AMR) AF: 0.406 AC: 6184 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4608 AN: 5142

South Asian (SAS) AF: 0.589 AC: 2826 AN: 4800

European-Finnish (FIN) AF: 0.288 AC: 3038 AN: 10556

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16473 AN: 67966

Other (OTH) AF: 0.282 AC: 597 AN: 2114

Alfa AF: 0.236 Hom.: 622

Bravo AF: 0.277

Asia WGS AF: 0.672 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.9
DANN	Benign	0.73
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs1408806; hg19: chr9-12531726;