ENST00000536914.1:n.337-83875T>C

Variant names:

• chr12-68150654-T-C
• rs11177074
• ENST00000536914.1:n.337-83875T>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-83875T>C		intron_variant	Intron 5 of 5	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;