chr12-33114747-A-G

Variant names:

• chr12-33114747-A-G
• rs1846629

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 0.383 in 151,956 control chromosomes in the GnomAD database, including 14,868 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 0.38 (14868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58096 AN: 151838 Hom.: 14853 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.383 AC: 58166 AN: 151956 Hom.: 14868 Cov.: 32 AF XY: 0.386 AC XY: 28653 AN XY: 74292

African (AFR) AF: 0.679 AC: 28114 AN: 41434

American (AMR) AF: 0.354 AC: 5403 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3462

East Asian (EAS) AF: 0.796 AC: 4115 AN: 5168

South Asian (SAS) AF: 0.479 AC: 2302 AN: 4808

European-Finnish (FIN) AF: 0.206 AC: 2185 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14061 AN: 67924

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.186 Hom.: 490

Bravo AF: 0.410

Asia WGS AF: 0.628 AC: 2178 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.80
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1846629; hg19: chr12-33267681;