rs12194046

Variant names:

• chr6-112668007-C-T
• rs12194046

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 0.0996 in 152,256 control chromosomes in the GnomAD database, including 811 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 0.10 (811 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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 (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0997 AC: 15168 AN: 152138 Hom.: 810 Cov.: 33

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0996 AC: 15169 AN: 152256 Hom.: 811 Cov.: 33 AF XY: 0.100 AC XY: 7458 AN XY: 74436

Gnomad4 AFR AF: 0.0510

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0742

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.111

Alfa AF: 0.104 Hom.: 145

Bravo AF: 0.0946

Asia WGS AF: 0.0680 AC: 236 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	0.39
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12194046; hg19: chr6-112989209;