12-68160508-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-74021G>C		intron_variant	Intron 5 of 5	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

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 v4.3

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;