rs754853086
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_033118.4(MYLK2):āc.21A>Gā(p.Ala7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000296 in 1,551,498 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 (ā ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000032 ( 0 hom. )
Consequence
MYLK2
NM_033118.4 synonymous
NM_033118.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.572
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 20-31819601-A-G is Benign according to our data. Variant chr20-31819601-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 227627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-31819601-A-G is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.572 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 45 AD,Digenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYLK2 | NM_033118.4 | c.21A>G | p.Ala7= | synonymous_variant | 2/13 | ENST00000375985.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYLK2 | ENST00000375985.5 | c.21A>G | p.Ala7= | synonymous_variant | 2/13 | 1 | NM_033118.4 | P1 | |
MYLK2 | ENST00000375994.6 | c.21A>G | p.Ala7= | synonymous_variant | 1/12 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156516Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82338
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GnomAD4 exome AF: 0.0000322 AC: 45AN: 1399288Hom.: 0 Cov.: 31 AF XY: 0.0000217 AC XY: 15AN XY: 690132
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 20, 2015 | p.Ala7Ala in exon 2 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2020 | 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. - |
Hypertrophic cardiomyopathy 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 27, 2023 | - - |
Computational scores
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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