chr12-69187442-C-A

Variant names:

• chr12-69187442-C-A
• rs12367448

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 0.137 in 151,626 control chromosomes in the GnomAD database, including 1,475 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 0.14 (1475 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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: 0.137 AC: 20740 AN: 151508 Hom.: 1478 Cov.: 29

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.137 AC: 20730 AN: 151626 Hom.: 1475 Cov.: 29 AF XY: 0.137 AC XY: 10180 AN XY: 74084

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.129

Alfa AF: 0.129 Hom.: 1380

Bravo AF: 0.133

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12367448; hg19: chr12-69581222;