9-121822636-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001139442.2(TTLL11):c.2084G>A(p.Arg695His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,384,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001139442.2 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTLL11 | NM_001139442.2 | c.2084G>A | p.Arg695His | missense_variant | 9/9 | ENST00000321582.11 | NP_001132914.2 | |
TTLL11 | NM_001386833.1 | c.431G>A | p.Arg144His | missense_variant | 4/4 | NP_001373762.1 | ||
TTLL11 | XM_047422825.1 | c.1508G>A | p.Arg503His | missense_variant | 8/8 | XP_047278781.1 | ||
TTLL11 | XR_001746188.2 | n.2244G>A | non_coding_transcript_exon_variant | 9/10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000276 AC: 4AN: 144914Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000443 AC: 5AN: 112878Hom.: 0 AF XY: 0.0000340 AC XY: 2AN XY: 58770
GnomAD4 exome AF: 0.0000210 AC: 26AN: 1239696Hom.: 0 Cov.: 32 AF XY: 0.0000149 AC XY: 9AN XY: 606050
GnomAD4 genome AF: 0.0000276 AC: 4AN: 144914Hom.: 0 Cov.: 32 AF XY: 0.0000283 AC XY: 2AN XY: 70666
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.2354G>A (p.R785H) alteration is located in exon 9 (coding exon 9) of the TTLL11 gene. This alteration results from a G to A substitution at nucleotide position 2354, causing the arginine (R) at amino acid position 785 to be replaced by a histidine (H). 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