rs727503305
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_033118.4(MYLK2):c.1284C>T(p.Gly428=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,256 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 (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
MYLK2
NM_033118.4 synonymous
NM_033118.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.253
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 20-31830878-C-T is Benign according to our data. Variant chr20-31830878-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 164508.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.253 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 25 AD,Digenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYLK2 | NM_033118.4 | c.1284C>T | p.Gly428= | synonymous_variant | 9/13 | ENST00000375985.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYLK2 | ENST00000375985.5 | c.1284C>T | p.Gly428= | synonymous_variant | 9/13 | 1 | NM_033118.4 | P1 | |
MYLK2 | ENST00000375994.6 | c.1284C>T | p.Gly428= | synonymous_variant | 8/12 | 1 | P1 | ||
MYLK2 | ENST00000468730.1 | n.222C>T | non_coding_transcript_exon_variant | 2/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151688Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251280Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135812
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461568Hom.: 0 Cov.: 46 AF XY: 0.0000206 AC XY: 15AN XY: 727078
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151688Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74094
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 17, 2014 | Gly428Gly in exon 9 of MYLK2: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. - |
Hypertrophic cardiomyopathy 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 05, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at