12-57047383-T-TAAG
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_005379.4(MYO1A):c.349_350insCTT(p.Ser116dup) variant causes a inframe insertion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
MYO1A
NM_005379.4 inframe_insertion
NM_005379.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.42
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 Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_005379.4. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 5/28 | ENST00000300119.8 | NP_005370.1 | |
MYO1A | NM_001256041.2 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 6/29 | NP_001242970.1 | ||
MYO1A | XM_011538373.3 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 5/25 | XP_011536675.1 | ||
MYO1A | XM_047428876.1 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 6/29 | XP_047284832.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 5/28 | 1 | NM_005379.4 | ENSP00000300119 | P1 | |
MYO1A | ENST00000442789.6 | c.349_350insCTT | p.Ser116dup | inframe_insertion | 6/29 | 1 | ENSP00000393392 | P1 | ||
MYO1A | ENST00000492945.5 | c.-21+2503_-21+2504insCTT | intron_variant | 4 | ENSP00000452229 | |||||
MYO1A | ENST00000554234.5 | c.-91_-90insCTT | 5_prime_UTR_variant, NMD_transcript_variant | 2/24 | 5 | ENSP00000451033 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autosomal dominant nonsyndromic hearing loss 48 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | May 01, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at