rs17056706

Variant names:

• chr5-159343747-C-T
• rs17056706
• ENST00000515337.1:n.746-3769C>T

Variant summary

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

The ENST00000515337.1(IL12B-AS1):​n.746-3769C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,010 control chromosomes in the GnomAD database, including 15,210 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 0.44 (15210 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	NR_037889.1		n.746-3769C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000515337.1	TSL:2	n.746-3769C>T		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.325-3769C>T		intron	N/A
	IL12B-AS1	ENST00000764988.1		n.567-10257C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66241 AN: 151892 Hom.: 15187 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.436 AC: 66330 AN: 152010 Hom.: 15210 Cov.: 32 AF XY: 0.444 AC XY: 32974 AN XY: 74290

African (AFR) AF: 0.557 AC: 23079 AN: 41444

American (AMR) AF: 0.446 AC: 6813 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2459 AN: 5168

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4818

European-Finnish (FIN) AF: 0.463 AC: 4884 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24389 AN: 67968

Other (OTH) AF: 0.404 AC: 852 AN: 2108

Alfa AF: 0.376 Hom.: 14222

Bravo AF: 0.441

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.57
PhyloP100		-0.62

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: rs17056706;

hg19: chr5-158770755;