chr19-36003395-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001039876.3(SYNE4):āc.1157G>Cā(p.Arg386Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R386Q) has been classified as Likely benign.
Frequency
Consequence
NM_001039876.3 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 |
---|---|---|---|---|---|---|---|
SYNE4 | NM_001039876.3 | c.1157G>C | p.Arg386Pro | missense_variant | 8/8 | ENST00000324444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE4 | ENST00000324444.9 | c.1157G>C | p.Arg386Pro | missense_variant | 8/8 | 5 | NM_001039876.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152034Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248566Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134972
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727174
GnomAD4 genome AF: 0.000164 AC: 25AN: 152034Hom.: 0 Cov.: 31 AF XY: 0.000202 AC XY: 15AN XY: 74252
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 21, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 28, 2024 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at