12-100426307-A-G

Variant names:

• chr12-100426307-A-G
• rs12296850

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 0.0898 in 152,222 control chromosomes in the GnomAD database, including 795 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 0.090 (795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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: 0.0897 AC: 13647 AN: 152104 Hom.: 790 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0638

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.0898 AC: 13662 AN: 152222 Hom.: 795 Cov.: 32 AF XY: 0.0906 AC XY: 6743 AN XY: 74420

African (AFR) AF: 0.121 AC: 5030 AN: 41530

American (AMR) AF: 0.0637 AC: 974 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1239 AN: 5182

South Asian (SAS) AF: 0.186 AC: 894 AN: 4812

European-Finnish (FIN) AF: 0.0545 AC: 578 AN: 10610

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0665 AC: 4521 AN: 68002

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.0736 Hom.: 1805

Bravo AF: 0.0904

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.59
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs12296850; hg19: chr12-100820085;