12-33928192-A-G

Variant names:

• chr12-33928192-A-G
• rs3898966

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 0.787 in 152,160 control chromosomes in the GnomAD database, including 47,299 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 0.79 (47299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.849 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: 0.787 AC: 119711 AN: 152042 Hom.: 47263 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.787 AC: 119804 AN: 152160 Hom.: 47299 Cov.: 32 AF XY: 0.789 AC XY: 58678 AN XY: 74394

African (AFR) AF: 0.746 AC: 30954 AN: 41504

American (AMR) AF: 0.814 AC: 12441 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3472

East Asian (EAS) AF: 0.837 AC: 4322 AN: 5166

South Asian (SAS) AF: 0.871 AC: 4210 AN: 4832

European-Finnish (FIN) AF: 0.803 AC: 8504 AN: 10588

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54073 AN: 67994

Other (OTH) AF: 0.797 AC: 1685 AN: 2114

Alfa AF: 0.808 Hom.: 65687

Bravo AF: 0.786

Asia WGS AF: 0.834 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.52
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3898966; hg19: chr12-34081127;