rs12895389
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152592.6(SYNE3):c.2727+6142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,272 control chromosomes in the GnomAD database, including 1,237 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.12 ( 1237 hom., cov: 33)
Consequence
SYNE3
NM_152592.6 intron
NM_152592.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.542
Genes affected
SYNE3 (HGNC:19861): (spectrin repeat containing nuclear envelope family member 3) Enables actin filament binding activity and cytoskeleton-nuclear membrane anchor activity. Involved in cytoskeleton organization; establishment of protein localization to membrane; and regulation of cell shape. Located in nuclear membrane. Part of meiotic nuclear membrane microtubule tethering complex. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNE3 | NM_152592.6 | c.2727+6142C>T | intron_variant | ENST00000682763.1 | |||
SYNE3 | NM_001363692.2 | c.2712+6142C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE3 | ENST00000682763.1 | c.2727+6142C>T | intron_variant | NM_152592.6 | P4 | ||||
SYNE3 | ENST00000334258.9 | c.2727+6142C>T | intron_variant | 1 | P4 | ||||
SYNE3 | ENST00000554873.5 | c.1998+6142C>T | intron_variant | 5 | |||||
SYNE3 | ENST00000557275.5 | c.2712+6142C>T | intron_variant | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.125 AC: 18961AN: 152154Hom.: 1237 Cov.: 33
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.124 AC: 18955AN: 152272Hom.: 1237 Cov.: 33 AF XY: 0.121 AC XY: 8983AN XY: 74458
GnomAD4 genome
?
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33
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74458
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324
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at