1-109475644-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001040709.2(SYPL2):c.193C>T(p.Arg65Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040709.2 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 |
---|---|---|---|---|---|---|---|---|
SYPL2 | NM_001040709.2 | c.193C>T | p.Arg65Cys | missense_variant | Exon 3 of 6 | ENST00000369872.4 | NP_001035799.1 | |
SYPL2 | XM_011541283.3 | c.193C>T | p.Arg65Cys | missense_variant | Exon 3 of 7 | XP_011539585.1 | ||
SYPL2 | XM_011541284.3 | c.193C>T | p.Arg65Cys | missense_variant | Exon 3 of 6 | XP_011539586.1 | ||
SYPL2 | XM_011541285.2 | c.193C>T | p.Arg65Cys | missense_variant | Exon 3 of 5 | XP_011539587.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249560Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135390
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461846Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727226
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.193C>T (p.R65C) alteration is located in exon 3 (coding exon 3) of the SYPL2 gene. This alteration results from a C to T substitution at nucleotide position 193, causing the arginine (R) at amino acid position 65 to be replaced by a cysteine (C). 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