2-112913801-G-C

Position:

• chr2-112913801-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014439.4(IL37):​c.92G>C​(p.Gly31Ala) variant causes a missense 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G31V) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL37 NM_014439.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

IL37 (HGNC:15563): (interleukin 37) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine can bind to, and may be a ligand for interleukin 18 receptor (IL18R1/IL-1Rrp). This cytokine also binds to interleukin 18 binding protein (IL18BP), an inhibitory binding protein of interleukin 18 (IL18), and subsequently forms a complex with IL18 receptor beta subunit, and through which it inhibits the activity of IL18. This gene along with eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. Five alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0629299).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL37	NM_014439.4	c.92G>C	p.Gly31Ala	missense_variant	3/6	ENST00000263326.8	NP_055254.2
IL37	NM_173204.2	c.92G>C	p.Gly31Ala	missense_variant	3/5		NP_775296.1
IL37	NM_173202.2	c.82+707G>C		intron_variant			NP_775294.1
IL37	NM_173203.2	c.82+707G>C		intron_variant			NP_775295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL37	ENST00000263326.8	c.92G>C	p.Gly31Ala	missense_variant	3/6	1	NM_014439.4	ENSP00000263326.3
IL37	ENST00000353225.7	c.92G>C	p.Gly31Ala	missense_variant	2/4	1		ENSP00000309208.3
IL37	ENST00000352179.7	c.82+707G>C		intron_variant		1		ENSP00000263327.3
IL37	ENST00000349806.7	c.82+707G>C		intron_variant		1		ENSP00000263328.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1 AN: 1461154 Hom.: 0 Cov.: 43 AF XY: 0.00 AC XY: 0 AN XY: 726912

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

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	0.095
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	11
DANN	Benign	0.70
DEOGEN2	Benign	0.0013	T;.
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.56	T;T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.063	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.55	N;N
PrimateAI	Benign	0.24	T
PROVEAN	Benign	0.16	N;N
REVEL	Benign	0.075
Sift	Benign	1.0	T;T
Sift4G	Benign	0.46	T;T
Polyphen		0.48	P;P
Vest4		0.18
MutPred		0.096		Loss of catalytic residue at A30 (P = 0.0609);Loss of catalytic residue at A30 (P = 0.0609);
MVP		0.30
MPC		0.094
ClinPred		0.17	T
GERP RS		1.9
Varity_R		0.059
gMVP		0.081

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		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: rs3811046; hg19: chr2-113671378;