rs201894544
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001082538.3(TCTN1):c.1471A>T(p.Ile491Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,614,036 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001082538.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCTN1 | NM_001082538.3 | c.1471A>T | p.Ile491Phe | missense_variant | 12/15 | ENST00000397659.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCTN1 | ENST00000397659.9 | c.1471A>T | p.Ile491Phe | missense_variant | 12/15 | 1 | NM_001082538.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00130 AC: 197AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000365 AC: 91AN: 249436Hom.: 0 AF XY: 0.000259 AC XY: 35AN XY: 135332
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461816Hom.: 0 Cov.: 30 AF XY: 0.000110 AC XY: 80AN XY: 727218
GnomAD4 genome ? AF: 0.00132 AC: 201AN: 152220Hom.: 1 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 06, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 30, 2020 | - - |
Joubert syndrome 13 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 02, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at