chr6-152236853-G-A
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_182961.4(SYNE1):c.20163C>T(p.Asn6721Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,968 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 Likely benign (★★).
Frequency
Consequence
NM_182961.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- autosomal recessive ataxia, Beauce typeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Orphanet, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
- arthrogryposis multiplex congenita 3, myogenic typeInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Emery-Dreifuss muscular dystrophy 4, autosomal dominantInheritance: AD Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina
- autosomal dominant Emery-Dreifuss muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal recessive myogenic arthrogryposis multiplex congenitaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.20163C>T | p.Asn6721Asn | synonymous_variant | Exon 109 of 146 | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.20163C>T | p.Asn6721Asn | synonymous_variant | Exon 109 of 146 | 1 | NM_182961.4 | ENSP00000356224.5 | ||
SYNE1 | ENST00000423061.6 | c.19950C>T | p.Asn6650Asn | synonymous_variant | Exon 108 of 146 | 1 | ENSP00000396024.1 | |||
SYNE1 | ENST00000367256.9 | n.3855C>T | non_coding_transcript_exon_variant | Exon 24 of 61 | 1 | |||||
SYNE1 | ENST00000409694.6 | n.3747C>T | non_coding_transcript_exon_variant | Exon 22 of 59 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152092Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000398 AC: 10AN: 251426 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727240 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74280 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
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SYNE1: BP4, BP7 -
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Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
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SYNE1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at