14-64053144-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_182914.3(SYNE2):c.9231G>A(p.Pro3077=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,614,092 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P3077P) has been classified as Likely benign.
Frequency
Consequence
NM_182914.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNE2 | NM_182914.3 | c.9231G>A | p.Pro3077= | synonymous_variant | 48/116 | ENST00000555002.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE2 | ENST00000555002.6 | c.9231G>A | p.Pro3077= | synonymous_variant | 48/116 | 1 | NM_182914.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152180Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000722 AC: 18AN: 249166Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135340
GnomAD4 exome AF: 0.0000889 AC: 130AN: 1461794Hom.: 0 Cov.: 37 AF XY: 0.0000866 AC XY: 63AN XY: 727194
GnomAD4 genome AF: 0.000368 AC: 56AN: 152298Hom.: 1 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SYNE2: BP4, BP7 - |
Emery-Dreifuss muscular dystrophy 5, autosomal dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at