rs367694491
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_015140.4(TTLL12):c.1774G>C(p.Gly592Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000071 in 1,407,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G592S) has been classified as Uncertain significance.
Frequency
Consequence
NM_015140.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTLL12 | NM_015140.4 | c.1774G>C | p.Gly592Arg | missense_variant | Exon 13 of 14 | ENST00000216129.7 | NP_055955.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTLL12 | ENST00000216129.7 | c.1774G>C | p.Gly592Arg | missense_variant | Exon 13 of 14 | 1 | NM_015140.4 | ENSP00000216129.6 | ||
TTLL12 | ENST00000494035.1 | c.37G>C | p.Gly13Arg | missense_variant | Exon 3 of 4 | 2 | ENSP00000476297.1 | |||
TTLL12 | ENST00000484711.1 | n.905G>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000599 AC: 1AN: 166874Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 88622
GnomAD4 exome AF: 7.10e-7 AC: 1AN: 1407480Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 695270
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at