chr12-43147696-A-G

Variant names:

• chr12-43147696-A-G
• rs733312

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 0.214 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.279 AC: 11575 AN: 41494

American (AMR) AF: 0.196 AC: 2997 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1283 AN: 5190

South Asian (SAS) AF: 0.120 AC: 579 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1721 AN: 10604

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13308 AN: 67998

Other (OTH) AF: 0.213 AC: 451 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.5
DANN	Benign	0.90
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs733312; hg19: chr12-43541499;