6-167340442-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031949.5(TTLL2):c.542C>T(p.Thr181Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000861 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031949.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTLL2 | ENST00000239587.10 | c.542C>T | p.Thr181Met | missense_variant | Exon 3 of 3 | 1 | NM_031949.5 | ENSP00000239587.5 | ||
TTLL2 | ENST00000515138.1 | n.542C>T | non_coding_transcript_exon_variant | Exon 3 of 6 | 1 | ENSP00000424130.1 | ||||
TTLL2 | ENST00000649884.1 | c.323C>T | p.Thr108Met | missense_variant | Exon 2 of 2 | ENSP00000497040.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251462Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135898
GnomAD4 exome AF: 0.0000903 AC: 132AN: 1461890Hom.: 0 Cov.: 36 AF XY: 0.0000935 AC XY: 68AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.542C>T (p.T181M) alteration is located in exon 3 (coding exon 3) of the TTLL2 gene. This alteration results from a C to T substitution at nucleotide position 542, causing the threonine (T) at amino acid position 181 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at