rs733312

Variant names:

• chr12-43147696-A-G
• rs733312

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 0.214 in 152,180 control chromosomes in the GnomAD database, including 3,650 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 0.21 (3650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.214 AC: 32579 AN: 152062 Hom.: 3639 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.214 AC: 32625 AN: 152180 Hom.: 3650 Cov.: 32 AF XY: 0.212 AC XY: 15748 AN XY: 74406

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.213

Alfa AF: 0.207 Hom.: 421

Bravo AF: 0.220

Asia WGS AF: 0.214 AC: 740 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.5
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733312; hg19: chr12-43541499;