rs3181032

Variant names:

• chr12-68162395-A-C
• rs3181032
• ENST00000536914.1:n.337-72134A>C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-72134A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 152,280 control chromosomes in the GnomAD database, including 502 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 0.054 (502 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 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.337-72134A>C		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8169 AN: 152162 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.00885

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0537 AC: 8183 AN: 152280 Hom.: 502 Cov.: 32 AF XY: 0.0561 AC XY: 4174 AN XY: 74462

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.0821

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.00885

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0357 Hom.: 176

Bravo AF: 0.0552

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181032; hg19: chr12-68556175;