rs12296850

Positions:

• chr12-100426307-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0637

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0545

Gnomad4 NFE AF: 0.0665

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0704 Hom.: 659

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12296850; hg19: chr12-100820085;