5-159433628-T-C

Variant names:

• chr5-159433628-T-C
• rs10515802
• ENST00000635333.1:n.524+9527T>C

Variant summary

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

The ENST00000636261.1(IL12B-AS1):​n.367+9498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,850 control chromosomes in the GnomAD database, including 5,011 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 0.24 (5011 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000636261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636261.1. 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.524+9527T>C		intron	N/A
	IL12B-AS1	ENST00000636261.1	TSL:4	n.367+9498T>C		intron	N/A
	IL12B-AS1	ENST00000764988.1		n.881+9527T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35632 AN: 151730 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.235 AC: 35695 AN: 151850 Hom.: 5011 Cov.: 32 AF XY: 0.229 AC XY: 16966 AN XY: 74236

African (AFR) AF: 0.400 AC: 16551 AN: 41386

American (AMR) AF: 0.152 AC: 2322 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.122 AC: 626 AN: 5138

South Asian (SAS) AF: 0.152 AC: 731 AN: 4802

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10558

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12831 AN: 67912

Other (OTH) AF: 0.211 AC: 445 AN: 2110

Alfa AF: 0.197 Hom.: 4222

Bravo AF: 0.244

Asia WGS AF: 0.144 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.074
DANN	Benign	0.11
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10515802; hg19: chr5-158860636;