12-68154004-C-T

Position:

• chr12-68154004-C-T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-80525C>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 0.127 in 152,172 control chromosomes in the GnomAD database, including 1,831 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 0.13 (1831 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-80525C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19362 AN: 152052 Hom.: 1829 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19381 AN: 152172 Hom.: 1831 Cov.: 32 AF XY: 0.129 AC XY: 9572 AN XY: 74396

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0876

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0855

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.117

Alfa AF: 0.115 Hom.: 253

Bravo AF: 0.132

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.21
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069728; hg19: chr12-68547784;