rs1833754

Variant names:

• chr5-159391919-T-C
• rs1833754
• ENST00000635333.1:n.283-614T>C

Variant summary

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

The ENST00000641150.1(IL12B-AS1):​n.533-24605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,204 control chromosomes in the GnomAD database, including 1,495 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 0.12 (1495 hom., cov: 33)
• Consequence: IL12B-AS1 ENST00000641150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.207 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.283-614T>C		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.533-24605T>C		intron	N/A
	IL12B-AS1	ENST00000648969.1		n.54-24605T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17602 AN: 152086 Hom.: 1485 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0881

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.116 AC: 17648 AN: 152204 Hom.: 1495 Cov.: 33 AF XY: 0.117 AC XY: 8686 AN XY: 74428

African (AFR) AF: 0.211 AC: 8752 AN: 41488

American (AMR) AF: 0.176 AC: 2687 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5184

South Asian (SAS) AF: 0.142 AC: 685 AN: 4828

European-Finnish (FIN) AF: 0.0512 AC: 543 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0489 AC: 3326 AN: 68024

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.0743 Hom.: 569

Bravo AF: 0.134

Asia WGS AF: 0.168 AC: 582 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	5.7
DANN	Benign	0.38
PhyloP100		1.7

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: rs1833754;

hg19: chr5-158818927;