15-99130137-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145728.3(SYNM):c.1777C>T(p.Pro593Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145728.3 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 |
---|---|---|---|---|---|---|---|---|
SYNM | NM_145728.3 | c.1777C>T | p.Pro593Ser | missense_variant | Exon 4 of 4 | ENST00000336292.11 | NP_663780.2 | |
SYNM | NM_015286.6 | c.1777C>T | p.Pro593Ser | missense_variant | Exon 4 of 5 | NP_056101.5 | ||
SYNM | XM_017022035.2 | c.1777C>T | p.Pro593Ser | missense_variant | Exon 4 of 5 | XP_016877524.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249046Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135148
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461656Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727098
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1777C>T (p.P593S) alteration is located in exon 4 (coding exon 4) of the SYNM gene. This alteration results from a C to T substitution at nucleotide position 1777, causing the proline (P) at amino acid position 593 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