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GeneBe

16-3068239-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001376923.1(IL32):c.201A>G(p.Pro67=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,592,332 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 17 hom. )

Consequence

IL32
NM_001376923.1 splice_region, synonymous

Scores

2
Splicing: ADA: 0.00008440
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.381
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-3068239-A-G is Benign according to our data. Variant chr16-3068239-A-G is described in ClinVar as [Benign]. Clinvar id is 710340.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.381 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL32NM_001376923.1 linkuse as main transcriptc.201A>G p.Pro67= splice_region_variant, synonymous_variant 6/7 ENST00000525643.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL32ENST00000525643.7 linkuse as main transcriptc.201A>G p.Pro67= splice_region_variant, synonymous_variant 6/71 NM_001376923.1 A2P24001-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00308
AC:
468
AN:
152158
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00111
Gnomad ASJ
AF:
0.00461
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00782
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00479
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00280
AC:
594
AN:
211768
Hom.:
3
AF XY:
0.00285
AC XY:
325
AN XY:
113836
show subpopulations
Gnomad AFR exome
AF:
0.000388
Gnomad AMR exome
AF:
0.000693
Gnomad ASJ exome
AF:
0.00356
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000112
Gnomad FIN exome
AF:
0.00646
Gnomad NFE exome
AF:
0.00429
Gnomad OTH exome
AF:
0.00296
GnomAD4 exome
AF:
0.00354
AC:
5092
AN:
1440056
Hom.:
17
Cov.:
31
AF XY:
0.00351
AC XY:
2507
AN XY:
714250
show subpopulations
Gnomad4 AFR exome
AF:
0.000302
Gnomad4 AMR exome
AF:
0.000727
Gnomad4 ASJ exome
AF:
0.00420
Gnomad4 EAS exome
AF:
0.0000257
Gnomad4 SAS exome
AF:
0.0000841
Gnomad4 FIN exome
AF:
0.00783
Gnomad4 NFE exome
AF:
0.00397
Gnomad4 OTH exome
AF:
0.00248
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00307
AC:
468
AN:
152276
Hom.:
4
Cov.:
32
AF XY:
0.00302
AC XY:
225
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.000553
Gnomad4 AMR
AF:
0.00111
Gnomad4 ASJ
AF:
0.00461
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00782
Gnomad4 NFE
AF:
0.00479
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00362
Hom.:
7
Bravo
AF:
0.00212
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
0.71
Dann
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000084
dbscSNV1_RF
Benign
0.0080
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

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

Other links and lift over

dbSNP: rs140322567; hg19: chr16-3118240; API