Variant chr2-112913801-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014439.4(IL37):c.92G>A(p.Gly31Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,154 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. )

Consequence

IL37
NM_014439.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.51

Variant links:

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]

IL37 links:

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ACMG classification

Classification made for transcript

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=0.084692985).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL37	NM_014439.4 linkuse as main transcript	c.92G>A	p.Gly31Glu	missense_variant	3/6	ENST00000263326.8	NP_055254.2	Q9NZH6-1
IL37	NM_173204.2 linkuse as main transcript	c.92G>A	p.Gly31Glu	missense_variant	3/5		NP_775296.1	Q9NZH6-3
IL37	NM_173202.2 linkuse as main transcript	c.82+707G>A		intron_variant			NP_775294.1	Q9NZH6-4
IL37	NM_173203.2 linkuse as main transcript	c.82+707G>A		intron_variant			NP_775295.1	Q9NZH6-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL37	ENST00000263326.8 linkuse as main transcript	c.92G>A	p.Gly31Glu	missense_variant	3/6	1	NM_014439.4	ENSP00000263326.3	Q9NZH6-1
IL37	ENST00000353225.7 linkuse as main transcript	c.92G>A	p.Gly31Glu	missense_variant	2/4	1		ENSP00000309208.3	Q9NZH6-3
IL37	ENST00000352179.7 linkuse as main transcript	c.82+707G>A		intron_variant		1		ENSP00000263327.3	Q9NZH6-4
IL37	ENST00000349806.7 linkuse as main transcript	c.82+707G>A		intron_variant		1		ENSP00000263328.3	Q9NZH6-5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000400

AC:

AN:

249698

Hom.:

AF XY:

0.00000741

AC XY:

AN XY:

134910

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000165

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461154

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726912

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000224

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.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.48

DEOGEN2

Benign

0.0012

T;.

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.52

T;T

M_CAP

Benign

0.0053

MetaRNN

Benign

0.085

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.20

N;N

PrimateAI

Benign

0.24

PROVEAN

Benign

0.60

N;N

REVEL

Benign

0.072

Sift

Benign

0.18

T;T

Sift4G

Benign

0.60

T;T

Polyphen

0.48

P;P

Vest4

0.17

MutPred

0.12

Loss of catalytic residue at A30 (P = 0.0373);Loss of catalytic residue at A30 (P = 0.0373);

MVP

0.35

MPC

0.11

ClinPred

0.13

GERP RS

1.9

Varity_R

0.060

gMVP

0.048

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over