9-12531726-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;