chr12-68160508-G-C

Variant names:

• chr12-68160508-G-C
• rs2069707
• ENST00000536914.1:n.337-74021G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-74021G>C variant causes a intron 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
• Clinical Significance: drug response no assertion criteria provided O:1
• Conservation: PhyloP100: -1.44
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-74021G>C		intron	N/A

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

African (AFR) AF: 0.0134 AC: 556 AN: 41428

American (AMR) AF: 0.0427 AC: 650 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.00604 AC: 29 AN: 4800

European-Finnish (FIN) AF: 0.0298 AC: 315 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4184 AN: 67954

Other (OTH) AF: 0.0429 AC: 90 AN: 2098

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

Jan 16, 2007

OMIM

Significance: drug response

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2069707; hg19: chr12-68554288;