rs1005224
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015072.5(TTLL5):c.656-106T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 856,848 control chromosomes in the GnomAD database, including 185,211 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.60 ( 28706 hom., cov: 30)
Exomes 𝑓: 0.66 ( 156505 hom. )
Consequence
TTLL5
NM_015072.5 intron
NM_015072.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.783
Genes affected
TTLL5 (HGNC:19963): (tubulin tyrosine ligase like 5) This gene encodes a member of the tubulin tyrosine ligase like protein family. This protein interacts with two glucocorticoid receptor coactivators, transcriptional intermediary factor 2 and steroid receptor coactivator 1. This protein may function as a coregulator of glucocorticoid receptor mediated gene induction and repression. This protein may also function as an alpha tubulin polyglutamylase.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTLL5 | NM_015072.5 | c.656-106T>A | intron_variant | ENST00000298832.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTLL5 | ENST00000298832.14 | c.656-106T>A | intron_variant | 1 | NM_015072.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.601 AC: 91177AN: 151726Hom.: 28691 Cov.: 30
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GnomAD4 exome AF: 0.660 AC: 465085AN: 705006Hom.: 156505 AF XY: 0.656 AC XY: 240964AN XY: 367066
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GnomAD4 genome ? AF: 0.601 AC: 91235AN: 151842Hom.: 28706 Cov.: 30 AF XY: 0.603 AC XY: 44768AN XY: 74204
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at