16-1992038-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004209.6(SYNGR3):c.164C>T(p.Pro55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,428,584 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P55R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004209.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNGR3 | ENST00000248121.7 | c.164C>T | p.Pro55Leu | missense_variant | Exon 2 of 4 | 1 | NM_004209.6 | ENSP00000248121.2 | ||
SYNGR3 | ENST00000568896.1 | c.284C>T | p.Pro95Leu | missense_variant | Exon 3 of 4 | 5 | ENSP00000454756.1 | |||
SYNGR3 | ENST00000563869.1 | c.96C>T | p.Pro32Pro | synonymous_variant | Exon 2 of 4 | 2 | ENSP00000455344.1 | |||
SYNGR3 | ENST00000562045 | c.-102C>T | 5_prime_UTR_variant | Exon 1 of 3 | 2 | ENSP00000455577.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1428584Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 708010
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.