chr12-110640499-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6BP7BS1
The NM_001082538.3(TCTN1):c.960C>T(p.Cys320Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000613 in 1,614,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001082538.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCTN1 | ENST00000397659.9 | c.960C>T | p.Cys320Cys | synonymous_variant | Exon 8 of 15 | 1 | NM_001082538.3 | ENSP00000380779.4 | ||
TCTN1 | ENST00000551590.5 | c.960C>T | p.Cys320Cys | synonymous_variant | Exon 8 of 15 | 1 | ENSP00000448735.1 | |||
TCTN1 | ENST00000397655.7 | c.918C>T | p.Cys306Cys | synonymous_variant | Exon 8 of 15 | 1 | ENSP00000380775.3 | |||
TCTN1 | ENST00000397656.8 | n.*593C>T | non_coding_transcript_exon_variant | Exon 9 of 16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000480648.5 | n.*236C>T | non_coding_transcript_exon_variant | Exon 9 of 16 | 5 | ENSP00000437196.1 | ||||
TCTN1 | ENST00000495659.6 | n.*718C>T | non_coding_transcript_exon_variant | Exon 8 of 15 | 2 | ENSP00000436673.2 | ||||
TCTN1 | ENST00000397656.8 | n.*593C>T | 3_prime_UTR_variant | Exon 9 of 16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000480648.5 | n.*236C>T | 3_prime_UTR_variant | Exon 9 of 16 | 5 | ENSP00000437196.1 | ||||
TCTN1 | ENST00000495659.6 | n.*718C>T | 3_prime_UTR_variant | Exon 8 of 15 | 2 | ENSP00000436673.2 |
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000789 AC: 197AN: 249602Hom.: 0 AF XY: 0.000702 AC XY: 95AN XY: 135402
GnomAD4 exome AF: 0.000627 AC: 916AN: 1461882Hom.: 1 Cov.: 31 AF XY: 0.000624 AC XY: 454AN XY: 727238
GnomAD4 genome AF: 0.000479 AC: 73AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74484
ClinVar
Submissions by phenotype
Joubert syndrome 13 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
TCTN1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at