chr11-120327494-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001198671.2(TLCD5):c.53C>T(p.Ser18Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001198671.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLCD5 | NM_001198671.2 | c.53C>T | p.Ser18Leu | missense_variant | 2/3 | ENST00000375095.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLCD5 | ENST00000375095.3 | c.53C>T | p.Ser18Leu | missense_variant | 2/3 | 2 | NM_001198671.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251494Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135922
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727248
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2024 | The c.119C>T (p.S40L) alteration is located in exon 2 (coding exon 1) of the TMEM136 gene. This alteration results from a C to T substitution at nucleotide position 119, causing the serine (S) at amino acid position 40 to be replaced by a leucine (L). 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