NM_182961.4:c.25120-16G>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_182961.4(SYNE1):c.25120-16G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0068 in 1,613,292 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_182961.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.25120-16G>T | intron_variant | Intron 138 of 145 | 1 | NM_182961.4 | ENSP00000356224.5 | |||
SYNE1 | ENST00000354674.5 | c.1654-16G>T | intron_variant | Intron 10 of 17 | 5 | NM_001347702.2 | ENSP00000346701.4 |
Frequencies
GnomAD3 genomes AF: 0.00668 AC: 1016AN: 152160Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00822 AC: 2067AN: 251400Hom.: 19 AF XY: 0.00851 AC XY: 1157AN XY: 135878
GnomAD4 exome AF: 0.00682 AC: 9957AN: 1461014Hom.: 83 Cov.: 32 AF XY: 0.00711 AC XY: 5166AN XY: 726834
GnomAD4 genome AF: 0.00668 AC: 1017AN: 152278Hom.: 5 Cov.: 32 AF XY: 0.00700 AC XY: 521AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
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not provided Benign:1
SYNE1: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at