10-26067085-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017433.5(MYO3A):c.1053+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,550,540 control chromosomes in the GnomAD database, including 215,466 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_017433.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO3A | ENST00000642920.2 | c.1053+11C>T | intron_variant | Intron 11 of 34 | NM_017433.5 | ENSP00000495965.1 | ||||
MYO3A | ENST00000543632.5 | c.1053+11C>T | intron_variant | Intron 10 of 16 | 1 | ENSP00000445909.1 | ||||
MYO3A | ENST00000642197.1 | n.1257+11C>T | intron_variant | Intron 11 of 26 | ||||||
MYO3A | ENST00000647478.1 | n.1053+11C>T | intron_variant | Intron 10 of 29 | ENSP00000493932.1 |
Frequencies
GnomAD3 genomes AF: 0.475 AC: 71957AN: 151626Hom.: 17823 Cov.: 32
GnomAD3 exomes AF: 0.477 AC: 118648AN: 248680Hom.: 30005 AF XY: 0.488 AC XY: 65645AN XY: 134442
GnomAD4 exome AF: 0.526 AC: 735785AN: 1398796Hom.: 197638 Cov.: 24 AF XY: 0.526 AC XY: 368128AN XY: 699216
GnomAD4 genome AF: 0.474 AC: 71975AN: 151744Hom.: 17828 Cov.: 32 AF XY: 0.474 AC XY: 35149AN XY: 74154
ClinVar
Submissions by phenotype
not specified Benign:3
1053+11C>T in Intron 11 of MYO3A: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence and has been identified in 47.1% (3305/7020) of European American chromoso mes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs .washington.edu/EVS; dbSNP rs3824698). -
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Autosomal recessive nonsyndromic hearing loss 30 Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at