rs12301088

Variant names:

• chr12-68196168-C-T
• rs12301088
• XR_001749193.2:n.3118C>T

Variant summary

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

The XR_001749193.2(LOC105369818):​n.3118C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,016 control chromosomes in the GnomAD database, including 11,186 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 0.37 (11186 hom., cov: 31)
• Consequence: LOC105369818 XR_001749193.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 publications found

Genes affected

LOC105369818 (HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.3118C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-38361C>T		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55586 AN: 151898 Hom.: 11175 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.366 AC: 55600 AN: 152016 Hom.: 11186 Cov.: 31 AF XY: 0.358 AC XY: 26573 AN XY: 74320

African (AFR) AF: 0.221 AC: 9147 AN: 41468

American (AMR) AF: 0.348 AC: 5312 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1558 AN: 3464

East Asian (EAS) AF: 0.146 AC: 754 AN: 5168

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4810

European-Finnish (FIN) AF: 0.348 AC: 3681 AN: 10586

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32024 AN: 67942

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.399 Hom.: 2133

Bravo AF: 0.357

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.40
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs12301088; hg19: chr12-68589948;