rs779548300
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001114133.3(SYNPO2L):c.1571G>T(p.Gly524Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000508 in 1,573,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G524E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001114133.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNPO2L | NM_001114133.3 | c.1571G>T | p.Gly524Val | missense_variant | Exon 4 of 4 | ENST00000394810.3 | NP_001107605.1 | |
SYNPO2L | NM_024875.5 | c.899G>T | p.Gly300Val | missense_variant | Exon 2 of 2 | NP_079151.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNPO2L | ENST00000394810.3 | c.1571G>T | p.Gly524Val | missense_variant | Exon 4 of 4 | 1 | NM_001114133.3 | ENSP00000378289.2 | ||
SYNPO2L | ENST00000372873.8 | c.899G>T | p.Gly300Val | missense_variant | Exon 2 of 2 | 1 | ENSP00000361964.4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151938Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000155 AC: 3AN: 194064Hom.: 0 AF XY: 0.0000189 AC XY: 2AN XY: 105590
GnomAD4 exome AF: 0.00000492 AC: 7AN: 1421934Hom.: 0 Cov.: 35 AF XY: 0.00000852 AC XY: 6AN XY: 703824
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at