rs2193035

Positions:

• chr12-68190860-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-43669T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,228 control chromosomes in the GnomAD database, including 3,055 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 0.12 (3055 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

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

LOC105369818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369818	XR_001749193.2	n.3040+4916T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-43669T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18576 AN: 152110 Hom.: 3040 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.00857

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.122 AC: 18634 AN: 152228 Hom.: 3055 Cov.: 32 AF XY: 0.123 AC XY: 9180 AN XY: 74448

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.0517

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.0812

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.00857

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0777 Hom.: 556

Bravo AF: 0.134

Asia WGS AF: 0.149 AC: 516 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193035; hg19: chr12-68584640;