10-73648216-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_001114133.3(SYNPO2L):c.1436G>T(p.Arg479Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000519 in 1,580,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001114133.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNPO2L | NM_001114133.3 | c.1436G>T | p.Arg479Leu | missense_variant | Exon 4 of 4 | ENST00000394810.3 | NP_001107605.1 | |
SYNPO2L | NM_024875.5 | c.764G>T | p.Arg255Leu | 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.1436G>T | p.Arg479Leu | missense_variant | Exon 4 of 4 | 1 | NM_001114133.3 | ENSP00000378289.2 | ||
SYNPO2L | ENST00000372873.8 | c.764G>T | p.Arg255Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000361964.4 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000981 AC: 22AN: 224362Hom.: 0 AF XY: 0.0000650 AC XY: 8AN XY: 123076
GnomAD4 exome AF: 0.0000252 AC: 36AN: 1428304Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 19AN XY: 707610
GnomAD4 genome AF: 0.000302 AC: 46AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1436G>T (p.R479L) alteration is located in exon 4 (coding exon 4) of the SYNPO2L gene. This alteration results from a G to T substitution at nucleotide position 1436, causing the arginine (R) at amino acid position 479 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