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GeneBe

1-200900178-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001142569.3(INAVA):c.255C>T(p.Ile85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,140 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 4 hom. )

Consequence

INAVA
NM_001142569.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.68
Variant links:
Genes affected
INAVA (HGNC:25599): (innate immunity activator) Involved in several processes, including nucleotide-binding activity oligomerization domain containing 2 signaling pathway; positive regulation of cytokine production; and positive regulation of intracellular signal transduction. Located in cytoplasm and nucleus. Implicated in inflammatory bowel disease 29. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 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=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-200900178-C-T is Benign according to our data. Variant chr1-200900178-C-T is described in ClinVar as [Benign]. Clinvar id is 781798.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=-1.68 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
INAVANM_001142569.3 linkuse as main transcriptc.255C>T p.Ile85= synonymous_variant 4/10 ENST00000413687.3
INAVANM_018265.4 linkuse as main transcriptc.510C>T p.Ile170= synonymous_variant 4/10
INAVANM_001367289.1 linkuse as main transcriptc.255C>T p.Ile85= synonymous_variant 4/10
INAVANM_001367290.1 linkuse as main transcriptc.-281C>T 5_prime_UTR_variant 4/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
INAVAENST00000413687.3 linkuse as main transcriptc.255C>T p.Ile85= synonymous_variant 4/102 NM_001142569.3 P2Q3KP66-3
INAVAENST00000367342.8 linkuse as main transcriptc.552C>T p.Ile184= synonymous_variant 4/101 A2
INAVAENST00000451872.6 linkuse as main transcriptc.255C>T p.Ile85= synonymous_variant 4/53

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00104
AC:
158
AN:
152222
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00111
Gnomad ASJ
AF:
0.00778
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00137
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00104
AC:
260
AN:
251074
Hom.:
0
AF XY:
0.00104
AC XY:
141
AN XY:
135736
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.00153
Gnomad ASJ exome
AF:
0.00705
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.000943
Gnomad OTH exome
AF:
0.00277
GnomAD4 exome
AF:
0.00109
AC:
1594
AN:
1461800
Hom.:
4
Cov.:
31
AF XY:
0.00112
AC XY:
816
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.000896
Gnomad4 AMR exome
AF:
0.00174
Gnomad4 ASJ exome
AF:
0.00846
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.000325
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.000982
Gnomad4 OTH exome
AF:
0.00197
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00104
AC:
158
AN:
152340
Hom.:
0
Cov.:
33
AF XY:
0.00110
AC XY:
82
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.000216
Gnomad4 AMR
AF:
0.00111
Gnomad4 ASJ
AF:
0.00778
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00137
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00146
Hom.:
0
Bravo
AF:
0.000994
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00251
EpiControl
AF:
0.00190

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 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
0.70
Dann
Benign
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
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: rs34596202; hg19: chr1-200869306; COSMIC: COSV66257330; COSMIC: COSV66257330; API