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GeneBe

1-200891603-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The ENST00000367342.8(INAVA):c.105G>A(p.Arg35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,562,954 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. R35R) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0093 ( 18 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 25 hom. )

Consequence

INAVA
ENST00000367342.8 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.588
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 -15 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=-0.6).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-200891603-G-A is Benign according to our data. Variant chr1-200891603-G-A is described in ClinVar as [Benign]. Clinvar id is 709585.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=0.588 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00933 (1421/152338) while in subpopulation AFR AF= 0.0318 (1321/41572). AF 95% confidence interval is 0.0304. There are 18 homozygotes in gnomad4. There are 692 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
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 18 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
INAVANM_018265.4 linkuse as main transcriptc.63G>A p.Arg21= synonymous_variant 1/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
INAVAENST00000367342.8 linkuse as main transcriptc.105G>A p.Arg35= synonymous_variant 1/101 A2
INAVAENST00000451872.6 linkuse as main transcriptc.-10+201G>A intron_variant 3
INAVAENST00000532631.5 linkuse as main transcriptc.-95+201G>A intron_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00930
AC:
1415
AN:
152220
Hom.:
18
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0317
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00451
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.00765
GnomAD3 exomes
AF:
0.00270
AC:
510
AN:
189228
Hom.:
7
AF XY:
0.00206
AC XY:
211
AN XY:
102194
show subpopulations
Gnomad AFR exome
AF:
0.0361
Gnomad AMR exome
AF:
0.00162
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000459
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000233
Gnomad OTH exome
AF:
0.000237
GnomAD4 exome
AF:
0.00102
AC:
1436
AN:
1410616
Hom.:
25
Cov.:
31
AF XY:
0.000888
AC XY:
621
AN XY:
699300
show subpopulations
Gnomad4 AFR exome
AF:
0.0351
Gnomad4 AMR exome
AF:
0.00184
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000127
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000152
Gnomad4 OTH exome
AF:
0.00211
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00933
AC:
1421
AN:
152338
Hom.:
18
Cov.:
33
AF XY:
0.00929
AC XY:
692
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.0318
Gnomad4 AMR
AF:
0.00451
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000220
Gnomad4 OTH
AF:
0.00757
Alfa
AF:
0.000577
Hom.:
0
Bravo
AF:
0.0108

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 testingInvitaeOct 17, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
Cadd
Benign
11
Dann
Benign
0.93

Splicing

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: rs141245080; hg19: chr1-200860731; API