12-110645014-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):c.1379G>C(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 (★★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCTN1 | ENST00000397659.9 | c.1379G>C | p.Ser460Thr | missense_variant | Exon 12 of 15 | 1 | NM_001082538.3 | ENSP00000380779.4 | ||
TCTN1 | ENST00000551590.5 | c.1379G>C | p.Ser460Thr | missense_variant | Exon 12 of 15 | 1 | ENSP00000448735.1 | |||
TCTN1 | ENST00000397655.7 | c.1337G>C | p.Ser446Thr | missense_variant | Exon 12 of 15 | 1 | ENSP00000380775.3 | |||
TCTN1 | ENST00000397656.8 | n.*1012G>C | non_coding_transcript_exon_variant | Exon 13 of 16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000480648.5 | n.*655G>C | non_coding_transcript_exon_variant | Exon 13 of 16 | 5 | ENSP00000437196.1 | ||||
TCTN1 | ENST00000495659.6 | n.*1137G>C | non_coding_transcript_exon_variant | Exon 12 of 15 | 2 | ENSP00000436673.2 | ||||
TCTN1 | ENST00000397656.8 | n.*1012G>C | 3_prime_UTR_variant | Exon 13 of 16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000480648.5 | n.*655G>C | 3_prime_UTR_variant | Exon 13 of 16 | 5 | ENSP00000437196.1 | ||||
TCTN1 | ENST00000495659.6 | n.*1137G>C | 3_prime_UTR_variant | Exon 12 of 15 | 2 | ENSP00000436673.2 |
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 provided Benign:2
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Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at