12-68196168-C-T

Position:

• chr12-68196168-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105369818 (HGNC:):

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=-0.86).
• 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/exons	MANE	UniProt
LOC105369818	XR_001749193.2	n.3118C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-38361C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.404

Alfa AF: 0.405 Hom.: 2111

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12301088; hg19: chr12-68589948;