rs12316797

Positions:

• chr12-42766942-T-G

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 0.183 in 152,150 control chromosomes in the GnomAD database, including 2,958 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 0.18 (2958 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42766942T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27873 AN: 152032 Hom.: 2953 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.183 AC: 27901 AN: 152150 Hom.: 2958 Cov.: 32 AF XY: 0.186 AC XY: 13839 AN XY: 74384

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.178

Alfa AF: 0.137 Hom.: 2655

Bravo AF: 0.196

Asia WGS AF: 0.214 AC: 742 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	6.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12316797; hg19: chr12-43160744;