X-47574714-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006950.3(SYN1):c.1367C>G(p.Pro456Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000894 in 111,867 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006950.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYN1 | NM_006950.3 | c.1367C>G | p.Pro456Arg | missense_variant | 11/13 | ENST00000295987.13 | |
SYN1 | NM_133499.2 | c.1367C>G | p.Pro456Arg | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.1367C>G | p.Pro456Arg | missense_variant | 11/13 | 2 | NM_006950.3 | P3 | |
SYN1 | ENST00000340666.5 | c.1367C>G | p.Pro456Arg | missense_variant | 11/13 | 1 | A1 | ||
SYN1 | ENST00000640721.1 | c.44C>G | p.Pro15Arg | missense_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111867Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34091
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1071212Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 348494
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111867Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34091
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 23, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at