rs141278987
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002469.3(MYF6):āc.544A>Cā(p.Thr182Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000484 in 1,576,370 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0027 ( 2 hom., cov: 32)
Exomes š: 0.00026 ( 2 hom. )
Consequence
MYF6
NM_002469.3 missense
NM_002469.3 missense
Scores
2
5
11
Clinical Significance
Conservation
PhyloP100: 4.07
Genes affected
MYF6 (HGNC:7566): (myogenic factor 6) The protein encoded by this gene is a probable basic helix-loop-helix (bHLH) DNA binding protein involved in muscle differentiation. The encoded protein likely acts as a heterodimer with another bHLH protein. Defects in this gene are a cause of autosomal dominant centronuclear myopathy (ADCNM). [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.012334496).
BP6
?
Variant 12-80708548-A-C is Benign according to our data. Variant chr12-80708548-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 472757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 394 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYF6 | NM_002469.3 | c.544A>C | p.Thr182Pro | missense_variant | 2/3 | ENST00000228641.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYF6 | ENST00000228641.4 | c.544A>C | p.Thr182Pro | missense_variant | 2/3 | 1 | NM_002469.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00264 AC: 391AN: 148190Hom.: 2 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000672 AC: 169AN: 251476Hom.: 0 AF XY: 0.000493 AC XY: 67AN XY: 135918
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GnomAD4 exome AF: 0.000258 AC: 369AN: 1428048Hom.: 2 Cov.: 33 AF XY: 0.000232 AC XY: 165AN XY: 710530
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GnomAD4 genome ? AF: 0.00266 AC: 394AN: 148322Hom.: 2 Cov.: 32 AF XY: 0.00258 AC XY: 187AN XY: 72442
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal dominant centronuclear myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | - - |
MYF6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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