rs10878774

Positions:

• chr12-68186492-G-A

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-48037G>A 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 0.644 in 151,998 control chromosomes in the GnomAD database, including 32,279 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 0.64 (32279 hom., cov: 30)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369818	XR_001749193.2	n.3040+548G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-48037G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97783 AN: 151880 Hom.: 32235 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.644 AC: 97883 AN: 151998 Hom.: 32279 Cov.: 30 AF XY: 0.646 AC XY: 47989 AN XY: 74268

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.663

Alfa AF: 0.606 Hom.: 3599

Bravo AF: 0.658

Asia WGS AF: 0.776 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10878774; hg19: chr12-68580272;