10-95693879-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_015631.6(TCTN3):c.21G>A(p.Ala7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000551 in 1,551,700 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.
Frequency
Consequence
NM_015631.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCTN3 | NM_015631.6 | c.21G>A | p.Ala7= | synonymous_variant | 1/14 | ENST00000371217.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCTN3 | ENST00000371217.10 | c.21G>A | p.Ala7= | synonymous_variant | 1/14 | 1 | NM_015631.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00303 AC: 461AN: 152214Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000772 AC: 120AN: 155482Hom.: 0 AF XY: 0.000691 AC XY: 57AN XY: 82536
GnomAD4 exome AF: 0.000282 AC: 394AN: 1399368Hom.: 3 Cov.: 32 AF XY: 0.000248 AC XY: 171AN XY: 690192
GnomAD4 genome AF: 0.00303 AC: 461AN: 152332Hom.: 4 Cov.: 32 AF XY: 0.00297 AC XY: 221AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 01, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Orofacial-digital syndrome IV;C3553758:Joubert syndrome 18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at