rs151220474
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_032578.4(MYPN):c.1236C>A(p.Thr412=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000492 in 1,613,590 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T412T) has been classified as Likely benign.
Frequency
Consequence
NM_032578.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYPN | NM_032578.4 | c.1236C>A | p.Thr412= | synonymous_variant | 5/20 | ENST00000358913.10 | |
LOC107984240 | XR_001747479.2 | n.206-1740G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYPN | ENST00000358913.10 | c.1236C>A | p.Thr412= | synonymous_variant | 5/20 | 1 | NM_032578.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000601 AC: 151AN: 251318Hom.: 0 AF XY: 0.000677 AC XY: 92AN XY: 135818
GnomAD4 exome AF: 0.000487 AC: 712AN: 1461366Hom.: 0 Cov.: 31 AF XY: 0.000484 AC XY: 352AN XY: 727014
GnomAD4 genome AF: 0.000539 AC: 82AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000619 AC XY: 46AN XY: 74360
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1KK Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Apr 11, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 09, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Dilated cardiomyopathy 1KK;C4479186:MYPN-related myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at