rs141583132

Variant names:

• chr16-3068238-C-A
• rs141583132
• NM_001376923.1:c.200C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3068238-C-A
• chr16-3068238-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001376923.1(IL32):​c.200C>A​(p.Pro67Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL32 NM_001376923.1 missense, splice_region
• Scores: Splicing: ADA: 0.00004936
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

Genes affected

IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.087097794).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1	c.200C>A	p.Pro67Gln	missense_variant, splice_region_variant	Exon 6 of 7	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.200C>A	p.Pro67Gln	missense_variant, splice_region_variant	Exon 6 of 7	1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1440868 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 714728

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	0.016
DANN	Benign	0.56
DEOGEN2	Benign	0.044	.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0019	N
LIST_S2	Benign	0.51	.;.;T;.;.;.;.;.;.;T;.;.;.;.;.;.;T;.;T;.;T;T;T;T;T;T;T
M_CAP	Benign	0.0076	T
MetaRNN	Benign	0.087	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Benign	0.0	.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;N;.;.;.;.;.;.;N;.;.;.;.
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-1.9	N;N;N;D;N;N;N;D;N;N;N;N;N;N;N;N;N;N;D;N;D;N;N;N;N;N;N
REVEL	Benign	0.19
Sift	Uncertain	0.0060	D;D;D;D;D;D;D;D;D;D;D;T;D;D;T;D;T;T;D;D;D;D;D;D;T;T;T
Sift4G	Benign	0.33	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.90	P;P;.;P;P;P;P;P;P;.;P;.;P;P;.;P;.;.;.;P;P;.;P;P;.;.;.
Vest4		0.14
MutPred		0.30		.;Loss of loop (P = 0.0022);.;.;.;.;.;.;.;Loss of loop (P = 0.0022);.;.;.;.;.;Loss of loop (P = 0.0022);.;.;Loss of loop (P = 0.0022);.;.;.;Loss of loop (P = 0.0022);.;.;.;.;
MVP		0.41
MPC		0.35
ClinPred		0.15	T
GERP RS		-3.8
Varity_R		0.036
gMVP		0.0025

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000049
dbscSNV1_RF	Benign	0.060
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs141583132; hg19: chr16-3118239;