12-107167650-T-G

Position:

• chr12-107167650-T-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 0.468 in 151,912 control chromosomes in the GnomAD database, including 16,927 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 0.47 (16927 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 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: 0.468 AC: 71015 AN: 151794 Hom.: 16897 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.468 AC: 71113 AN: 151912 Hom.: 16927 Cov.: 31 AF XY: 0.466 AC XY: 34613 AN XY: 74202

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.482

Alfa AF: 0.442 Hom.: 29578

Bravo AF: 0.482

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11113204; hg19: chr12-107561428;