rs2467012

Positions:

• chr12-46061116-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 0.413 in 151,810 control chromosomes in the GnomAD database, including 13,389 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 0.41 (13389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62672 AN: 151692 Hom.: 13381 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.413 AC: 62704 AN: 151810 Hom.: 13389 Cov.: 32 AF XY: 0.420 AC XY: 31169 AN XY: 74224

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.403

Alfa AF: 0.290 Hom.: 744

Bravo AF: 0.402

Asia WGS AF: 0.497 AC: 1726 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2467012; hg19: chr12-46454899;