Variant 19-4817276-AAGGAGGAGGAGG-AAGGAGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The ENST00000248244.6(TICAM1):c.1096_1101del(p.Pro366_Pro367del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 1,603,258 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 27)

Exomes 𝑓: 0.00017 ( 1 hom. )

Consequence

TICAM1
ENST00000248244.6 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.993

Variant links:

Genes affected

TICAM1 (HGNC:18348): (TIR domain containing adaptor molecule 1) This gene encodes an adaptor protein containing a Toll/interleukin-1 receptor (TIR) homology domain, which is an intracellular signaling domain that mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. This protein is involved in native immunity against invading pathogens. It specifically interacts with toll-like receptor 3, but not with other TLRs, and this association mediates dsRNA induction of interferon-beta through activation of nuclear factor kappa-B, during an antiviral immune response. Mutations in this gene are associated with encephalopathy, acute, infection-induced. [provided by RefSeq, Jul 2020]

TICAM1 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;

BP6

Variant 19-4817276-AAGGAGG-A is Benign according to our data. Variant chr19-4817276-AAGGAGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 712940.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-4817276-AAGGAGG-A is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TICAM1	NM_182919.4 linkuse as main transcript	c.1096_1101del	p.Pro366_Pro367del	inframe_deletion	2/2	ENST00000248244.6	NP_891549.1
TICAM1	NM_001385678.1 linkuse as main transcript	c.1054_1059del	p.Pro352_Pro353del	inframe_deletion	3/3		NP_001372607.1
TICAM1	NM_001385679.1 linkuse as main transcript	c.961_966del	p.Pro321_Pro322del	inframe_deletion	2/2		NP_001372608.1
TICAM1	NM_001385680.1 linkuse as main transcript	c.454_459del	p.Pro152_Pro153del	inframe_deletion	3/3		NP_001372609.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TICAM1	ENST00000248244.6 linkuse as main transcript	c.1096_1101del	p.Pro366_Pro367del	inframe_deletion	2/2	1	NM_182919.4	ENSP00000248244	P1

Frequencies

GnomAD3 genomes

AF:

0.000129

AC:

AN:

147568

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000515

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000337

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000987

Gnomad SAS

AF:

0.000214

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000744

Gnomad OTH

AF:

0.000493

GnomAD3 exomes

AF:

0.000296

AC:

AN:

246324

Hom.:

AF XY:

0.000217

AC XY:

AN XY:

133478

show subpopulations

Gnomad AFR exome

AF:

0.000129

Gnomad AMR exome

AF:

0.00129

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000765

Gnomad SAS exome

AF:

0.000133

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000539

Gnomad OTH exome

AF:

0.000500

GnomAD4 exome

AF:

0.000167

AC:

243

AN:

1455572

Hom.:

AF XY:

0.000149

AC XY:

108

AN XY:

724160

show subpopulations

Gnomad4 AFR exome

AF:

0.000515

Gnomad4 AMR exome

AF:

0.00108

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00113

Gnomad4 SAS exome

AF:

0.0000698

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000849

Gnomad4 OTH exome

AF:

0.000532

GnomAD4 genome

AF:

0.000129

AC:

AN:

147686

Hom.:

Cov.:

AF XY:

0.000125

AC XY:

AN XY:

72068

show subpopulations

Gnomad4 AFR

AF:

0.0000513

Gnomad4 AMR

AF:

0.000337

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000989

Gnomad4 SAS

AF:

0.000214

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000744

Gnomad4 OTH

AF:

0.000487

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Herpes simplex encephalitis, susceptibility to, 4

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 25, 2024

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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