rs7132697

Positions:

• chr12-68139061-T-A

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-95468T>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 0.755 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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=-0.8).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-95468T>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.782

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7132697; hg19: chr12-68532841;