5-159357103-C-G

Variant names:

• chr5-159357103-C-G
• rs1363670
• ENST00000515337.1:n.953+2982C>G

Variant summary

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

The ENST00000515337.1(IL12B-AS1):​n.953+2982C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,232 control chromosomes in the GnomAD database, including 60,406 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 0.89 (60406 hom., cov: 31)
• Consequence: IL12B-AS1 ENST00000515337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 21 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.953+2982C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12B-AS1	ENST00000515337.1	TSL:2	n.953+2982C>G		intron	N/A
	IL12B-AS1	ENST00000635333.1	TSL:5	n.282+2982C>G		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.532+2982C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135195 AN: 152114 Hom.: 60342 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.889 AC: 135319 AN: 152232 Hom.: 60406 Cov.: 31 AF XY: 0.892 AC XY: 66388 AN XY: 74430

African (AFR) AF: 0.970 AC: 40320 AN: 41550

American (AMR) AF: 0.904 AC: 13818 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2973 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5190

South Asian (SAS) AF: 0.891 AC: 4302 AN: 4826

European-Finnish (FIN) AF: 0.860 AC: 9102 AN: 10588

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56736 AN: 67998

Other (OTH) AF: 0.888 AC: 1876 AN: 2112

Alfa AF: 0.863 Hom.: 7075

Bravo AF: 0.897

Asia WGS AF: 0.955 AC: 3321 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	0.78
DANN	Benign	0.48
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1363670; hg19: chr5-158784111;