chr12-68346352-C-G

Position:

• chr12-68346352-C-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 0.682 in 152,104 control chromosomes in the GnomAD database, including 35,689 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 0.68 (35689 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68346352C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02384	ENST00000539404.1	n.69-12688G>C		intron_variant		3
ENSG00000256273	ENST00000544089.1	n.240+1449C>G		intron_variant		2
LINC02384	ENST00000546086.1	n.154-12688G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103720 AN: 151986 Hom.: 35679 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.682 AC: 103778 AN: 152104 Hom.: 35689 Cov.: 32 AF XY: 0.681 AC XY: 50659 AN XY: 74354

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.688

Alfa AF: 0.676 Hom.: 3596

Bravo AF: 0.681

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7971639; hg19: chr12-68740132;