chr14-95417872-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152592.6(SYNE3):c.2882G>A(p.Arg961His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,050 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R961C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152592.6 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 |
---|---|---|---|---|---|---|---|---|---|---|
SYNE3 | ENST00000682763.1 | c.2882G>A | p.Arg961His | missense_variant | Exon 18 of 18 | NM_152592.6 | ENSP00000507501.1 | |||
SYNE3 | ENST00000334258.9 | c.2882G>A | p.Arg961His | missense_variant | Exon 17 of 17 | 1 | ENSP00000334308.4 | |||
SYNE3 | ENST00000557275.5 | c.2867G>A | p.Arg956His | missense_variant | Exon 17 of 17 | 2 | ENSP00000450562.1 | |||
SYNE3 | ENST00000554873.5 | c.2153G>A | p.Arg718His | missense_variant | Exon 13 of 13 | 5 | ENSP00000452154.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251476Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135906
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461890Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727244
GnomAD4 genome AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2882G>A (p.R961H) 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 2882, causing the arginine (R) at amino acid position 961 to be replaced by a histidine (H). 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