12-30333451-A-G

Variant names:

• chr12-30333451-A-G
• rs906115

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 0.232 in 152,162 control chromosomes in the GnomAD database, including 5,071 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 0.23 (5071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.232 AC: 35243 AN: 152044 Hom.: 5064 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 35287 AN: 152162 Hom.: 5071 Cov.: 32 AF XY: 0.232 AC XY: 17245 AN XY: 74408

African (AFR) AF: 0.413 AC: 17141 AN: 41480

American (AMR) AF: 0.183 AC: 2802 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5170

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1499 AN: 10598

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9965 AN: 68018

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.206 Hom.: 543

Bravo AF: 0.241

Asia WGS AF: 0.237 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs906115; hg19: chr12-30486384;