rs11177074

chr12-68150654-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.337-83875T>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 0.101 in 152,278 control chromosomes in the GnomAD database, including 982 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 0.10 (982 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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.337-83875T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15429 AN: 152160 Hom.: 982 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.101 AC: 15437 AN: 152278 Hom.: 982 Cov.: 32 AF XY: 0.103 AC XY: 7650 AN XY: 74468

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0854

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.0655

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0772 Hom.: 105

Bravo AF: 0.103

Asia WGS AF: 0.159 AC: 550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11177074; hg19: chr12-68544434;