ENST00000664175.2:n.1475C>T

Variant names:

• chr3-159997015-G-A
• rs2243143
• ENST00000664175.2:n.1475C>T

Variant summary

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

The ENST00000664175.2(IL12A-AS1):​n.1475C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,870 control chromosomes in the GnomAD database, including 14,578 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 0.43 (14578 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000664175.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 12 publications found

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A 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 (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1084+829C>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000664175.2	n.1475C>T		non_coding_transcript_exon_variant	Exon 3 of 3
IL12A-AS1	ENST00000740380.1	n.1655C>T		non_coding_transcript_exon_variant	Exon 2 of 2
IL12A-AS1	ENST00000740381.1	n.1842C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64852 AN: 151752 Hom.: 14560 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.427 AC: 64914 AN: 151870 Hom.: 14578 Cov.: 31 AF XY: 0.419 AC XY: 31071 AN XY: 74230

African (AFR) AF: 0.564 AC: 23343 AN: 41380

American (AMR) AF: 0.391 AC: 5967 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3464

East Asian (EAS) AF: 0.164 AC: 847 AN: 5166

South Asian (SAS) AF: 0.232 AC: 1114 AN: 4808

European-Finnish (FIN) AF: 0.377 AC: 3982 AN: 10552

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27233 AN: 67924

Other (OTH) AF: 0.406 AC: 857 AN: 2112

Alfa AF: 0.410 Hom.: 36313

Bravo AF: 0.441

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.34
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2243143; hg19: chr3-159714802;