chr12-110645014-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001082538.3(TCTN1):āc.1379G>Cā(p.Ser460Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000449 in 1,614,238 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S460R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001082538.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCTN1 | NM_001082538.3 | c.1379G>C | p.Ser460Thr | missense_variant | 12/15 | ENST00000397659.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCTN1 | ENST00000397659.9 | c.1379G>C | p.Ser460Thr | missense_variant | 12/15 | 1 | NM_001082538.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 352AN: 152230Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000581 AC: 145AN: 249560Hom.: 1 AF XY: 0.000554 AC XY: 75AN XY: 135400
GnomAD4 exome AF: 0.000254 AC: 372AN: 1461890Hom.: 2 Cov.: 30 AF XY: 0.000230 AC XY: 167AN XY: 727246
GnomAD4 genome AF: 0.00231 AC: 352AN: 152348Hom.: 1 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 04, 2015 | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at