9-12531726-C-G

Variant names:

• chr9-12531726-C-G
• rs1408806

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.282

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408806; hg19: chr9-12531726;