chr6-152330899-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_182961.4(SYNE1):c.13786T>A(p.Ser4596Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 1,614,046 control chromosomes in the GnomAD database, including 473,479 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_182961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.13786T>A | p.Ser4596Thr | missense_variant | Exon 78 of 146 | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.13786T>A | p.Ser4596Thr | missense_variant | Exon 78 of 146 | 1 | NM_182961.4 | ENSP00000356224.5 | ||
SYNE1 | ENST00000423061.6 | c.13573T>A | p.Ser4525Thr | missense_variant | Exon 77 of 146 | 1 | ENSP00000396024.1 | |||
SYNE1 | ENST00000490135.6 | n.1132T>A | non_coding_transcript_exon_variant | Exon 2 of 11 | 1 |
Frequencies
GnomAD3 genomes AF: 0.802 AC: 121997AN: 152102Hom.: 49213 Cov.: 32
GnomAD3 exomes AF: 0.780 AC: 195948AN: 251358Hom.: 77245 AF XY: 0.766 AC XY: 104127AN XY: 135878
GnomAD4 exome AF: 0.760 AC: 1110859AN: 1461826Hom.: 424207 Cov.: 65 AF XY: 0.755 AC XY: 549048AN XY: 727216
GnomAD4 genome AF: 0.802 AC: 122114AN: 152220Hom.: 49272 Cov.: 32 AF XY: 0.805 AC XY: 59939AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:7
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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not provided Benign:2
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Autosomal recessive ataxia, Beauce type Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
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Arthrogryposis multiplex congenita 3, myogenic type Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at