rs10045431

Variant names:

• chr5-159387525-A-C
• rs10045431
• ENST00000635333.1:n.283-5008A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-159387525-A-C
• chr5-159387525-A-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.533-28999A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,060 control chromosomes in the GnomAD database, including 46,796 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 0.78 (46796 hom., cov: 32)
• Consequence: IL12B-AS1 ENST00000641150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 83 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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.283-5008A>C		intron	N/A
	IL12B-AS1	ENST00000641150.1		n.533-28999A>C		intron	N/A
	IL12B-AS1	ENST00000648969.1		n.54-28999A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118711 AN: 151942 Hom.: 46727 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.782 AC: 118844 AN: 152060 Hom.: 46796 Cov.: 32 AF XY: 0.788 AC XY: 58590 AN XY: 74320

African (AFR) AF: 0.872 AC: 36233 AN: 41528

American (AMR) AF: 0.815 AC: 12445 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2274 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4674 AN: 5150

South Asian (SAS) AF: 0.836 AC: 4026 AN: 4816

European-Finnish (FIN) AF: 0.785 AC: 8287 AN: 10552

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48400 AN: 67960

Other (OTH) AF: 0.770 AC: 1624 AN: 2108

Alfa AF: 0.731 Hom.: 191328

Bravo AF: 0.787

Asia WGS AF: 0.884 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		-1.0

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: rs10045431;

hg19: chr5-158814533;