ENST00000515337.1:n.745+4467T>C

Variant names:

• chr5-159337470-T-C
• rs4921482
• ENST00000515337.1:n.745+4467T>C

Variant summary

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

The ENST00000515337.1(IL12B-AS1):​n.745+4467T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,992 control chromosomes in the GnomAD database, including 8,260 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 0.33 (8260 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 11 publications found

Genes affected

IL12B-AS1 (HGNC:58156):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515337.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	NR_037889.1		n.745+4467T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000515337.1	TSL:2	n.745+4467T>C		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.324+4467T>C		intron	N/A
	IL12B-AS1	ENST00000764988.1		n.566+4467T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49665 AN: 151874 Hom.: 8256 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.327 AC: 49690 AN: 151992 Hom.: 8260 Cov.: 32 AF XY: 0.327 AC XY: 24326 AN XY: 74290

African (AFR) AF: 0.297 AC: 12326 AN: 41444

American (AMR) AF: 0.345 AC: 5277 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2180 AN: 5164

South Asian (SAS) AF: 0.373 AC: 1802 AN: 4828

European-Finnish (FIN) AF: 0.319 AC: 3374 AN: 10564

Middle Eastern (MID) AF: 0.352 AC: 102 AN: 290

European-Non Finnish (NFE) AF: 0.334 AC: 22660 AN: 67936

Other (OTH) AF: 0.347 AC: 732 AN: 2110

Alfa AF: 0.265 Hom.: 1127

Bravo AF: 0.327

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4921482; hg19: chr5-158764478;