chr11-134356379-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001370461.1(GLB1L2):c.637C>T(p.Pro213Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370461.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLB1L2 | NM_001370461.1 | c.637C>T | p.Pro213Ser | missense_variant | 6/19 | ENST00000535456.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLB1L2 | ENST00000535456.7 | c.637C>T | p.Pro213Ser | missense_variant | 6/19 | 1 | NM_001370461.1 | P1 | |
GLB1L2 | ENST00000529077.5 | n.941C>T | non_coding_transcript_exon_variant | 3/22 | 1 | ||||
GLB1L2 | ENST00000531081.5 | n.177C>T | non_coding_transcript_exon_variant | 2/4 | 4 | ||||
GLB1L2 | ENST00000533324.2 | n.119C>T | non_coding_transcript_exon_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251432Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459760Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726364
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.637C>T (p.P213S) alteration is located in exon 6 (coding exon 6) of the GLB1L2 gene. This alteration results from a C to T substitution at nucleotide position 637, causing the proline (P) at amino acid position 213 to be replaced by a serine (S). 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