rs3741097
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370461.1(GLB1L2):c.1680C>A(p.Thr560=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,524 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_001370461.1 synonymous
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 | UniProt |
---|---|---|---|---|---|---|---|
GLB1L2 | NM_001370461.1 | c.1680C>A | p.Thr560= | synonymous_variant | 17/19 | ENST00000535456.7 | |
GLB1L2 | NM_001370460.1 | c.1842C>A | p.Thr614= | synonymous_variant | 18/20 | ||
GLB1L2 | NM_138342.4 | c.1680C>A | p.Thr560= | synonymous_variant | 17/20 | ||
GLB1L2 | XR_007062523.1 | n.1754C>A | non_coding_transcript_exon_variant | 17/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLB1L2 | ENST00000535456.7 | c.1680C>A | p.Thr560= | synonymous_variant | 17/19 | 1 | NM_001370461.1 | P1 | |
GLB1L2 | ENST00000529077.5 | n.4009C>A | non_coding_transcript_exon_variant | 18/22 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251422Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726688
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at