12-47529233-T-C

Variant names:

• chr12-47529233-T-C
• rs7307902

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 0.306 in 151,924 control chromosomes in the GnomAD database, including 8,713 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 0.31 (8713 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46478 AN: 151806 Hom.: 8715 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.306 AC: 46485 AN: 151924 Hom.: 8713 Cov.: 31 AF XY: 0.307 AC XY: 22784 AN XY: 74244

African (AFR) AF: 0.100 AC: 4164 AN: 41490

American (AMR) AF: 0.252 AC: 3852 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2627 AN: 5158

South Asian (SAS) AF: 0.394 AC: 1900 AN: 4820

European-Finnish (FIN) AF: 0.390 AC: 4095 AN: 10500

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27545 AN: 67914

Other (OTH) AF: 0.316 AC: 666 AN: 2110

Alfa AF: 0.365 Hom.: 32589

Bravo AF: 0.285

Asia WGS AF: 0.392 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.23
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7307902; hg19: chr12-47923016;