rs12350534

chr9-86943149-C-T

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 0.0774 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0580

Gnomad4 NFE AF: 0.0788

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0761 Hom.: 605

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12350534; hg19: chr9-89558064;