16-1991999-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004209.6(SYNGR3):c.125C>T(p.Pro42Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000693 in 1,442,518 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_004209.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.125C>T | p.Pro42Leu | missense_variant | Exon 2 of 4 | 1 | NM_004209.6 | ENSP00000248121.2 | ||
SYNGR3 | ENST00000568896.1 | c.245C>T | p.Pro82Leu | missense_variant | Exon 3 of 4 | 5 | ENSP00000454756.1 | |||
SYNGR3 | ENST00000563869.1 | c.57C>T | p.Ala19Ala | synonymous_variant | Exon 2 of 4 | 2 | ENSP00000455344.1 | |||
SYNGR3 | ENST00000562045 | c.-141C>T | 5_prime_UTR_variant | Exon 1 of 3 | 2 | ENSP00000455577.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1442518Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 716136
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.125C>T (p.P42L) alteration is located in exon 2 (coding exon 2) of the SYNGR3 gene. This alteration results from a C to T substitution at nucleotide position 125, causing the proline (P) at amino acid position 42 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