Variant chr1-200891603-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000367342.8(INAVA):c.105G>C(p.Arg35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00675 in 1,562,952 control chromosomes in the GnomAD database, including 51 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 0.0043 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0070 ( 51 hom. )

Consequence

INAVA
ENST00000367342.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

INAVA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 1-200891603-G-C is Benign according to our data. Variant chr1-200891603-G-C is described in ClinVar as [Benign]. Clinvar id is 779223.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.588 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INAVA	NM_018265.4 linkuse as main transcript	c.63G>C	p.Arg21=	synonymous_variant	1/10		NP_060735.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	Appris
INAVA	ENST00000367342.8 linkuse as main transcript	c.105G>C	p.Arg35=	synonymous_variant	1/10	1	ENSP00000356311	A2
INAVA	ENST00000451872.6 linkuse as main transcript	c.-10+201G>C		intron_variant		3	ENSP00000397255
INAVA	ENST00000532631.5 linkuse as main transcript	c.-95+201G>C		intron_variant		3	ENSP00000431682

Frequencies

GnomAD3 genomes

AF:

0.00431

AC:

656

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000392

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000620

Gnomad FIN

AF:

0.00339

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00801

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00499

AC:

944

AN:

189228

Hom.:

AF XY:

0.00483

AC XY:

494

AN XY:

102194

show subpopulations

Gnomad AFR exome

AF:

0.00114

Gnomad AMR exome

AF:

0.000479

Gnomad ASJ exome

AF:

0.000176

Gnomad EAS exome

AF:

0.0000758

Gnomad SAS exome

AF:

0.000550

Gnomad FIN exome

AF:

0.00448

Gnomad NFE exome

AF:

0.00926

Gnomad OTH exome

AF:

0.00522

GnomAD4 exome

AF:

0.00702

AC:

9896

AN:

1410608

Hom.:

Cov.:

AF XY:

0.00671

AC XY:

4693

AN XY:

699296

show subpopulations

Gnomad4 AFR exome

AF:

0.000862

Gnomad4 AMR exome

AF:

0.000544

Gnomad4 ASJ exome

AF:

0.000440

Gnomad4 EAS exome

AF:

0.0000554

Gnomad4 SAS exome

AF:

0.000355

Gnomad4 FIN exome

AF:

0.00549

Gnomad4 NFE exome

AF:

0.00852

Gnomad4 OTH exome

AF:

0.00425

GnomAD4 genome

AF:

0.00431

AC:

656

AN:

152344

Hom.:

Cov.:

AF XY:

0.00392

AC XY:

292

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00339

Gnomad4 NFE

AF:

0.00801

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00162

Hom.:

Bravo

AF:

0.00402

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.85

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over