12-68160508-G-C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):n.337-74021G>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 0.0403 in 151,952 control chromosomes in the GnomAD database, including 186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

• Frequency: Genomes: 𝑓 0.040 (186 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: drug response no assertion criteria provided O:1
• Conservation: PhyloP100: -1.44

Genes affected

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.06 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-74021G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0404 AC: 6129 AN: 151834 Hom.: 186 Cov.: 31

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00604

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0434

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

GnomAD4 genome AF: 0.0403 AC: 6129 AN: 151952 Hom.: 186 Cov.: 31 AF XY: 0.0383 AC XY: 2840 AN XY: 74238

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0427

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00604

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0616

Gnomad4 OTH AF: 0.0429

Alfa AF: 0.0236 Hom.: 14

Bravo AF: 0.0402

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Significance: drug response

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Hepatitis C virus infection, response to therapy of Other:1

drug response, no assertion criteria provided

literature only

OMIM

Jan 16, 2007

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.11
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069707; hg19: chr12-68554288;