12-107167650-T-G

Variant names:

• chr12-107167650-T-G
• rs11113204

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.539 AC: 22329 AN: 41412

American (AMR) AF: 0.509 AC: 7757 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2158 AN: 5154

South Asian (SAS) AF: 0.359 AC: 1726 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3931 AN: 10546

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30314 AN: 67956

Other (OTH) AF: 0.482 AC: 1016 AN: 2108

Alfa AF: 0.450 Hom.: 64497

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11113204; hg19: chr12-107561428;