chr12-68150654-T-C

Variant names:

• chr12-68150654-T-C
• rs11177074
• ENST00000536914.1:n.337-83875T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-83875T>C		intron	N/A

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

African (AFR) AF: 0.164 AC: 6814 AN: 41530

American (AMR) AF: 0.0793 AC: 1213 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3470

East Asian (EAS) AF: 0.0854 AC: 443 AN: 5188

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4828

European-Finnish (FIN) AF: 0.0523 AC: 556 AN: 10624

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0655 AC: 4455 AN: 68028

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0800 Hom.: 116

Bravo AF: 0.103

Asia WGS AF: 0.159 AC: 550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.7
DANN	Benign	0.53
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11177074; hg19: chr12-68544434;