chr12-57036808-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005379.4(MYO1A):c.2238C>T(p.Ser746=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,614,070 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 (★). Synonymous variant affecting the same amino acid position (i.e. S746S) has been classified as Likely benign.
Frequency
Consequence
NM_005379.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.2238C>T | p.Ser746= | synonymous_variant | 21/28 | ENST00000300119.8 | |
MYO1A | NM_001256041.2 | c.2238C>T | p.Ser746= | synonymous_variant | 22/29 | ||
MYO1A | XM_047428876.1 | c.2238C>T | p.Ser746= | synonymous_variant | 22/29 | ||
MYO1A | XM_011538373.3 | c.2238C>T | p.Ser746= | synonymous_variant | 21/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.2238C>T | p.Ser746= | synonymous_variant | 21/28 | 1 | NM_005379.4 | P1 | |
MYO1A | ENST00000442789.6 | c.2238C>T | p.Ser746= | synonymous_variant | 22/29 | 1 | P1 | ||
MYO1A | ENST00000554234.5 | c.1752C>T | p.Ser584= | synonymous_variant, NMD_transcript_variant | 17/24 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251440Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135882
GnomAD4 exome AF: 0.000111 AC: 163AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.000117 AC XY: 85AN XY: 727246
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 29, 2014 | Ser746Ser in exon 21 of MYO1A: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at