12-107136216-G-A

Position:

• chr12-107136216-G-A

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 0.608 in 152,046 control chromosomes in the GnomAD database, including 28,429 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 0.61 (28429 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.608 AC: 92295 AN: 151926 Hom.: 28401 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.608 AC: 92374 AN: 152046 Hom.: 28429 Cov.: 32 AF XY: 0.613 AC XY: 45508 AN XY: 74292

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.602

Alfa AF: 0.617 Hom.: 55998

Bravo AF: 0.604

Asia WGS AF: 0.731 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778536; hg19: chr12-107529994;