12-107167650-T-G

Variant names:

• chr12-107167650-T-G
• rs11113204

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;