rs2348080
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000367255.10(SYNE1):c.24450+28A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 1,613,058 control chromosomes in the GnomAD database, including 1,530 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.043 ( 171 hom., cov: 32)
Exomes 𝑓: 0.040 ( 1359 hom. )
Consequence
SYNE1
ENST00000367255.10 intron
ENST00000367255.10 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.470
Genes affected
SYNE1 (HGNC:17089): (spectrin repeat containing nuclear envelope protein 1) This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 6-152151525-T-A is Benign according to our data. Variant chr6-152151525-T-A is described in ClinVar as [Benign]. Clinvar id is 262189.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0429 (6536/152242) while in subpopulation AMR AF= 0.0505 (772/15300). AF 95% confidence interval is 0.0475. There are 171 homozygotes in gnomad4. There are 3183 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 6536 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_001347702.2 | c.915+28A>T | intron_variant | ENST00000354674.5 | NP_001334631.1 | |||
SYNE1 | NM_182961.4 | c.24450+28A>T | intron_variant | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000354674.5 | c.915+28A>T | intron_variant | 5 | NM_001347702.2 | ENSP00000346701 | ||||
SYNE1 | ENST00000367255.10 | c.24450+28A>T | intron_variant | 1 | NM_182961.4 | ENSP00000356224 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0428 AC: 6516AN: 152124Hom.: 170 Cov.: 32
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GnomAD3 exomes AF: 0.0383 AC: 9565AN: 249744Hom.: 233 AF XY: 0.0378 AC XY: 5107AN XY: 135158
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GnomAD4 exome AF: 0.0403 AC: 58928AN: 1460816Hom.: 1359 Cov.: 31 AF XY: 0.0398 AC XY: 28919AN XY: 726644
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GnomAD4 genome AF: 0.0429 AC: 6536AN: 152242Hom.: 171 Cov.: 32 AF XY: 0.0428 AC XY: 3183AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at