rs12146838

Variant names:

• chr12-91981819-A-T
• rs12146838

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 0.229 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.126 AC: 5233 AN: 41508

American (AMR) AF: 0.222 AC: 3391 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3470

East Asian (EAS) AF: 0.00655 AC: 34 AN: 5190

South Asian (SAS) AF: 0.0942 AC: 455 AN: 4830

European-Finnish (FIN) AF: 0.230 AC: 2439 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21229 AN: 67960

Other (OTH) AF: 0.266 AC: 561 AN: 2112

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12146838; hg19: chr12-92375595;