12-68153413-T-G

Position:

• chr12-68153413-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 0.755 in 152,036 control chromosomes in the GnomAD database, including 43,989 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 0.75 (43989 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68153413T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-81116T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114604 AN: 151918 Hom.: 43922 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.755 AC: 114732 AN: 152036 Hom.: 43989 Cov.: 31 AF XY: 0.752 AC XY: 55866 AN XY: 74300

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.782

Alfa AF: 0.709 Hom.: 4548

Bravo AF: 0.770

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193050; hg19: chr12-68547193;