6-152428357-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_182961.4(SYNE1):c.4824G>A(p.Ala1608=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,964 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A1608A) has been classified as Likely benign.
Frequency
Consequence
NM_182961.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.4824G>A | p.Ala1608= | synonymous_variant | 37/146 | ENST00000367255.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.4824G>A | p.Ala1608= | synonymous_variant | 37/146 | 1 | NM_182961.4 | P1 | |
SYNE1 | ENST00000423061.6 | c.4845G>A | p.Ala1615= | synonymous_variant | 37/146 | 1 | |||
SYNE1 | ENST00000461872.6 | n.5042G>A | non_coding_transcript_exon_variant | 35/55 | 1 | ||||
SYNE1 | ENST00000367253.8 | c.4824G>A | p.Ala1608= | synonymous_variant | 35/36 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251226Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135758
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461712Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727148
GnomAD4 genome AF: 0.000144 AC: 22AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74442
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 29, 2016 | - - |
Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at