22-43168025-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015140.4(TTLL12):c.1918G>A(p.Val640Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000403 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015140.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTLL12 | NM_015140.4 | c.1918G>A | p.Val640Ile | missense_variant | Exon 14 of 14 | ENST00000216129.7 | NP_055955.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTLL12 | ENST00000216129.7 | c.1918G>A | p.Val640Ile | missense_variant | Exon 14 of 14 | 1 | NM_015140.4 | ENSP00000216129.6 | ||
TTLL12 | ENST00000494035.1 | c.181G>A | p.Val61Ile | missense_variant | Exon 4 of 4 | 2 | ENSP00000476297.1 | |||
TTLL12 | ENST00000484711.1 | n.1049G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251066Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135714
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461594Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727120
GnomAD4 genome AF: 0.000125 AC: 19AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1918G>A (p.V640I) alteration is located in exon 14 (coding exon 14) of the TTLL12 gene. This alteration results from a G to A substitution at nucleotide position 1918, causing the valine (V) at amino acid position 640 to be replaced by an isoleucine (I). 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