12-68226017-G-T

Position:

• chr12-68226017-G-T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-8512G>T 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 0.163 in 150,744 control chromosomes in the GnomAD database, including 2,809 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 0.16 (2809 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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.337-8512G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24532 AN: 150628 Hom.: 2800 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0956

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.163 AC: 24566 AN: 150744 Hom.: 2809 Cov.: 32 AF XY: 0.174 AC XY: 12815 AN XY: 73604

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.0956

Gnomad4 OTH AF: 0.172

Alfa AF: 0.105 Hom.: 604

Bravo AF: 0.170

Asia WGS AF: 0.381 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
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: rs3814241; hg19: chr12-68619797;