12-124624381-A-G

Position:

• chr12-124624381-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 0.0866 in 152,246 control chromosomes in the GnomAD database, including 676 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 0.087 (676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 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: 0.0866 AC: 13172 AN: 152128 Hom.: 677 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0866 AC: 13189 AN: 152246 Hom.: 676 Cov.: 33 AF XY: 0.0843 AC XY: 6277 AN XY: 74448

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.0739

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0730 Hom.: 499

Bravo AF: 0.0877

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.83
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7959363; hg19: chr12-125108927;