12-68190765-A-G

Position:

• chr12-68190765-A-G

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-43764A>G 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 0.475 in 152,104 control chromosomes in the GnomAD database, including 18,644 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 0.48 (18644 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.3040+4821A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-43764A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72241 AN: 151986 Hom.: 18632 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.475 AC: 72276 AN: 152104 Hom.: 18644 Cov.: 32 AF XY: 0.464 AC XY: 34485 AN XY: 74352

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.517

Alfa AF: 0.541 Hom.: 9030

Bravo AF: 0.465

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2870951; hg19: chr12-68584545;