rs7132697

Variant names:

• chr12-68139061-T-A
• rs7132697
• ENST00000536914.1:n.337-95468T>A

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-95468T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,146 control chromosomes in the GnomAD database, including 44,113 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 0.76 (44113 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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.337-95468T>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114815 AN: 152028 Hom.: 44046 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.755 AC: 114943 AN: 152146 Hom.: 44113 Cov.: 32 AF XY: 0.753 AC XY: 55968 AN XY: 74350

African (AFR) AF: 0.870 AC: 36151 AN: 41538

American (AMR) AF: 0.765 AC: 11692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3443 AN: 5166

South Asian (SAS) AF: 0.848 AC: 4090 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6294 AN: 10560

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 48006 AN: 67988

Other (OTH) AF: 0.782 AC: 1653 AN: 2114

Alfa AF: 0.720 Hom.: 4971

Bravo AF: 0.770

Asia WGS AF: 0.796 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7132697; hg19: chr12-68532841;