14-64053053-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182914.3(SYNE2):āc.9140A>Gā(p.Lys3047Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_182914.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNE2 | NM_182914.3 | c.9140A>G | p.Lys3047Arg | missense_variant | 48/116 | ENST00000555002.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE2 | ENST00000555002.6 | c.9140A>G | p.Lys3047Arg | missense_variant | 48/116 | 1 | NM_182914.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000153 AC: 38AN: 249112Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135272
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461738Hom.: 0 Cov.: 37 AF XY: 0.0000234 AC XY: 17AN XY: 727138
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74512
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy 5, autosomal dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at