rs1558744

Variant names:

• chr12-68110812-G-A
• rs1558744
• ENST00000536914.1:n.336+84104G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.336+84104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,956 control chromosomes in the GnomAD database, including 13,208 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 0.40 (13208 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 39 publications found

Genes affected

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

ENSG00000301254 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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.336+84104G>A		intron_variant	Intron 5 of 5	5
ENSG00000301254	ENST00000777404.1	n.167+7547C>T		intron_variant	Intron 1 of 2
ENSG00000301254	ENST00000777405.1	n.187+7547C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61455 AN: 151838 Hom.: 13194 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.405 AC: 61502 AN: 151956 Hom.: 13208 Cov.: 31 AF XY: 0.395 AC XY: 29348 AN XY: 74270

African (AFR) AF: 0.522 AC: 21594 AN: 41398

American (AMR) AF: 0.293 AC: 4477 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1216 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5186

South Asian (SAS) AF: 0.187 AC: 903 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4033 AN: 10530

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27497 AN: 67970

Other (OTH) AF: 0.400 AC: 844 AN: 2108

Alfa AF: 0.393 Hom.: 40648

Bravo AF: 0.404

Asia WGS AF: 0.201 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1558744; hg19: chr12-68504592;