rs2561288

Variant names:

• chr3-159957140-T-C
• rs2561288
• ENST00000497452.5:n.1350+31957A>G

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.1350+31957A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,984 control chromosomes in the GnomAD database, including 22,367 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 0.54 (22367 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497452.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.1350+31957A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.1350+31957A>G		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.778+31957A>G		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.837+31957A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81418 AN: 151864 Hom.: 22321 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.536 AC: 81526 AN: 151984 Hom.: 22367 Cov.: 32 AF XY: 0.530 AC XY: 39378 AN XY: 74272

African (AFR) AF: 0.599 AC: 24801 AN: 41432

American (AMR) AF: 0.519 AC: 7925 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2216 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5168

South Asian (SAS) AF: 0.512 AC: 2472 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10548

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.537 AC: 36467 AN: 67968

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.556 Hom.: 5322

Bravo AF: 0.542

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		0.060

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2561288;

hg19: chr3-159674928;