rs12350534

Variant names:

• chr9-86943149-C-T
• rs12350534

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 0.0774 in 152,200 control chromosomes in the GnomAD database, including 465 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 0.077 (465 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0775 AC: 11780 AN: 152082 Hom.: 464 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0774 AC: 11786 AN: 152200 Hom.: 465 Cov.: 33 AF XY: 0.0768 AC XY: 5716 AN XY: 74416

African (AFR) AF: 0.103 AC: 4282 AN: 41518

American (AMR) AF: 0.0663 AC: 1013 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 175 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4822

European-Finnish (FIN) AF: 0.0580 AC: 615 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0788 AC: 5362 AN: 68004

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0773 Hom.: 1007

Bravo AF: 0.0785

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.1
DANN	Benign	0.60
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12350534; hg19: chr9-89558064;