chr12-68152957-T-C

Position:

• chr12-68152957-T-C

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 0.752 in 152,110 control chromosomes in the GnomAD database, including 43,629 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 (43629 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68152957T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-81572T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114187 AN: 151992 Hom.: 43563 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.752 AC: 114314 AN: 152110 Hom.: 43629 Cov.: 32 AF XY: 0.749 AC XY: 55692 AN XY: 74364

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.778

Alfa AF: 0.737 Hom.: 6356

Bravo AF: 0.766

Asia WGS AF: 0.796 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181034; hg19: chr12-68546737;