chr14-95417899-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152592.6(SYNE3):c.2855G>A(p.Ser952Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152592.6 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 |
---|---|---|---|---|---|---|---|---|---|---|
SYNE3 | ENST00000682763.1 | c.2855G>A | p.Ser952Asn | missense_variant | Exon 18 of 18 | NM_152592.6 | ENSP00000507501.1 | |||
SYNE3 | ENST00000334258.9 | c.2855G>A | p.Ser952Asn | missense_variant | Exon 17 of 17 | 1 | ENSP00000334308.4 | |||
SYNE3 | ENST00000557275.5 | c.2840G>A | p.Ser947Asn | missense_variant | Exon 17 of 17 | 2 | ENSP00000450562.1 | |||
SYNE3 | ENST00000554873.5 | c.2126G>A | p.Ser709Asn | missense_variant | Exon 13 of 13 | 5 | ENSP00000452154.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000137 AC: 2AN: 1461882Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727242
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2855G>A (p.S952N) alteration is located in exon 17 (coding exon 17) of the SYNE3 gene. This alteration results from a G to A substitution at nucleotide position 2855, causing the serine (S) at amino acid position 952 to be replaced by an asparagine (N). 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