chr6-152395636-A-G
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4
The NM_182961.4(SYNE1):c.7592T>C(p.Ile2531Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000397 in 1,614,004 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 Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. I2531I) has been classified as Likely benign.
Frequency
Consequence
NM_182961.4 missense
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: Likely_benign. The variant received -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.7592T>C | p.Ile2531Thr | missense_variant | Exon 51 of 146 | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.7592T>C | p.Ile2531Thr | missense_variant | Exon 51 of 146 | 1 | NM_182961.4 | ENSP00000356224.5 | ||
SYNE1 | ENST00000423061.6 | c.7613T>C | p.Ile2538Thr | missense_variant | Exon 51 of 146 | 1 | ENSP00000396024.1 | |||
SYNE1 | ENST00000461872.6 | n.7810T>C | non_coding_transcript_exon_variant | Exon 49 of 55 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000239 AC: 6AN: 251180 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727222 show subpopulations
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74326 show subpopulations
ClinVar
Submissions by phenotype
not provided Uncertain:2
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- -
not specified Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at