5-159412209-C-T

Variant names:

• chr5-159412209-C-T
• rs1422878
• ENST00000635333.1:n.328-4315C>T

Variant summary

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

The ENST00000641150.1(IL12B-AS1):​n.533-4315C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,106 control chromosomes in the GnomAD database, including 8,859 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 0.34 (8859 hom., cov: 33)
• Consequence: IL12B-AS1 ENST00000641150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 9 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 (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641150.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000635333.1	TSL:5	n.328-4315C>T		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.533-4315C>T		intron	N/A
	IL12B-AS1	ENST00000648969.1		n.54-4315C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51721 AN: 151988 Hom.: 8843 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.340 AC: 51767 AN: 152106 Hom.: 8859 Cov.: 33 AF XY: 0.337 AC XY: 25026 AN XY: 74354

African (AFR) AF: 0.324 AC: 13440 AN: 41478

American (AMR) AF: 0.299 AC: 4564 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1934 AN: 5182

South Asian (SAS) AF: 0.375 AC: 1811 AN: 4830

European-Finnish (FIN) AF: 0.322 AC: 3399 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24597 AN: 67984

Other (OTH) AF: 0.345 AC: 731 AN: 2116

Alfa AF: 0.334 Hom.: 5189

Bravo AF: 0.337

Asia WGS AF: 0.398 AC: 1383 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	1.9
DANN	Benign	0.20
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1422878; hg19: chr5-158839217;