12-123671246-C-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_024809.5(TCTN2):c.6C>A(p.Gly2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TCTN2
NM_024809.5 synonymous
NM_024809.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.100
Genes affected
TCTN2 (HGNC:25774): (tectonic family member 2) This gene encodes a type I membrane protein that belongs to the tectonic family. Studies in mice suggest that this protein may be involved in hedgehog signaling, and essential for ciliogenesis. Mutations in this gene are associated with Meckel syndrome type 8. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 12-123671246-C-A is Benign according to our data. Variant chr12-123671246-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2166235.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.1 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TCTN2 | NM_024809.5 | c.6C>A | p.Gly2= | synonymous_variant | 1/18 | ENST00000303372.7 | NP_079085.2 | |
| TCTN2 | NM_001143850.3 | c.6C>A | p.Gly2= | synonymous_variant | 1/18 | NP_001137322.1 | ||
| TCTN2 | NM_001410989.1 | c.6C>A | p.Gly2= | synonymous_variant | 1/17 | NP_001397918.1 | ||
| TCTN2 | XM_017019974.2 | c.6C>A | p.Gly2= | synonymous_variant | 1/17 | XP_016875463.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TCTN2 | ENST00000303372.7 | c.6C>A | p.Gly2= | synonymous_variant | 1/18 | 1 | NM_024809.5 | ENSP00000304941 | P4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460668Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726606
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
1460668
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Cov.:
32
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0
AN XY:
726606
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.