12-68154443-T-C

Position:

• chr12-68154443-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-80086T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,952 control chromosomes in the GnomAD database, including 10,768 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 0.36 (10768 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-80086T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54234 AN: 151834 Hom.: 10761 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.357 AC: 54245 AN: 151952 Hom.: 10768 Cov.: 31 AF XY: 0.350 AC XY: 26023 AN XY: 74250

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.399

Alfa AF: 0.443 Hom.: 20757

Bravo AF: 0.346

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069727; hg19: chr12-68548223;