22-43051885-C-T
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 2P and 16B. PP3_ModerateBP6_Very_StrongBA1
The NM_012263.5(TTLL1):c.894G>A(p.Pro298Pro) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 1,613,604 control chromosomes in the GnomAD database, including 1,898 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_012263.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTLL1 | NM_012263.5 | c.894G>A | p.Pro298Pro | splice_region_variant, synonymous_variant | Exon 9 of 11 | ENST00000266254.12 | NP_036395.1 | |
TTLL1 | NR_027779.2 | n.1202G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 10 of 12 | ||||
TTLL1-AS1 | NR_125362.1 | n.1772-170C>T | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0331 AC: 5029AN: 151978Hom.: 127 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0335 AC: 8416AN: 251380 AF XY: 0.0341 show subpopulations
GnomAD4 exome AF: 0.0460 AC: 67294AN: 1461508Hom.: 1771 Cov.: 31 AF XY: 0.0449 AC XY: 32651AN XY: 727060 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0331 AC: 5028AN: 152096Hom.: 127 Cov.: 32 AF XY: 0.0327 AC XY: 2430AN XY: 74362 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, silent -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at