rs147832651
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_005379.4(MYO1A):c.2316C>T(p.Ala772Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,758 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 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
MYO1A
NM_005379.4 synonymous
NM_005379.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.962
Genes affected
MYO1A (HGNC:7595): (myosin IA) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional skeletal muscle myosin-1 (MYH1). Unconventional myosins contain the basic domains characteristic of conventional myosins and are further distinguished from class members by their tail domains. They function as actin-based molecular motors. Mutations in this gene have been associated with autosomal dominant deafness. Alternatively spliced variants have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 12-57036340-G-A is Benign according to our data. Variant chr12-57036340-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 178454.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.962 with no splicing effect.
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.2316C>T | p.Ala772Ala | synonymous_variant | 22/28 | ENST00000300119.8 | NP_005370.1 | |
MYO1A | NM_001256041.2 | c.2316C>T | p.Ala772Ala | synonymous_variant | 23/29 | NP_001242970.1 | ||
MYO1A | XM_047428876.1 | c.2316C>T | p.Ala772Ala | synonymous_variant | 23/29 | XP_047284832.1 | ||
MYO1A | XM_011538373.3 | c.2316C>T | p.Ala772Ala | synonymous_variant | 22/25 | XP_011536675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.2316C>T | p.Ala772Ala | synonymous_variant | 22/28 | 1 | NM_005379.4 | ENSP00000300119.3 | ||
MYO1A | ENST00000442789.6 | c.2316C>T | p.Ala772Ala | synonymous_variant | 23/29 | 1 | ENSP00000393392.2 | |||
MYO1A | ENST00000554234.5 | n.1830C>T | non_coding_transcript_exon_variant | 18/24 | 5 | ENSP00000451033.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251152Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135722
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461576Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727088
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74346
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
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 30, 2012 | Ala772Ala in Exon 22 of MYO1A: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 0.1% (2/3738) of Afri can American chromosomes from a broad population by the NHLBI Exome Sequencing P roject (http://evs.gs.washington.edu/EVS; dbSNP rs147832651). - |
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