6-152344136-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_182961.4(SYNE1):c.12170C>T(p.Pro4057Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000455 in 1,614,186 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P4057P) has been classified as Likely benign.
Frequency
Consequence
NM_182961.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.12170C>T | p.Pro4057Leu | missense_variant | 74/146 | ENST00000367255.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.12170C>T | p.Pro4057Leu | missense_variant | 74/146 | 1 | NM_182961.4 | P1 | |
SYNE1 | ENST00000423061.6 | c.11957C>T | p.Pro3986Leu | missense_variant | 73/146 | 1 | |||
SYNE1 | ENST00000471834.1 | n.5308C>T | non_coding_transcript_exon_variant | 17/19 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00263 AC: 401AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000612 AC: 154AN: 251474Hom.: 0 AF XY: 0.000486 AC XY: 66AN XY: 135912
GnomAD4 exome AF: 0.000228 AC: 333AN: 1461884Hom.: 1 Cov.: 34 AF XY: 0.000204 AC XY: 148AN XY: 727242
GnomAD4 genome AF: 0.00264 AC: 402AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.00255 AC XY: 190AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 26, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 24, 2016 | - - |
Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant;C5193121:Arthrogryposis multiplex congenita 3, myogenic type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 20, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at