rs12146838

chr12-91981819-A-T

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 0.229 in 152,146 control chromosomes in the GnomAD database, including 4,693 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 0.23 (4693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34887 AN: 152028 Hom.: 4697 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.229 AC: 34884 AN: 152146 Hom.: 4693 Cov.: 32 AF XY: 0.221 AC XY: 16457 AN XY: 74392

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.00655

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.266

Alfa AF: 0.273 Hom.: 739

Bravo AF: 0.226

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.4
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12146838; hg19: chr12-92375595;