rs113470661
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005379.4(MYO1A):c.2390C>T(p.Ser797Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 1,614,148 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005379.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.2390C>T | p.Ser797Phe | missense_variant | 23/28 | ENST00000300119.8 | |
MYO1A | NM_001256041.2 | c.2390C>T | p.Ser797Phe | missense_variant | 24/29 | ||
MYO1A | XM_047428876.1 | c.2390C>T | p.Ser797Phe | missense_variant | 24/29 | ||
MYO1A | XM_011538373.3 | c.2390C>T | p.Ser797Phe | missense_variant | 23/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.2390C>T | p.Ser797Phe | missense_variant | 23/28 | 1 | NM_005379.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00488 AC: 742AN: 152150Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00451 AC: 1135AN: 251450Hom.: 2 AF XY: 0.00433 AC XY: 588AN XY: 135904
GnomAD4 exome AF: 0.00611 AC: 8931AN: 1461880Hom.: 32 Cov.: 32 AF XY: 0.00600 AC XY: 4367AN XY: 727244
GnomAD4 genome ? AF: 0.00487 AC: 742AN: 152268Hom.: 5 Cov.: 32 AF XY: 0.00479 AC XY: 357AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:6
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Ser797Phe in Exon 23 of MYO1A: This variant is not expected to have clinical sig nificance because it has been identified in 0.7% (47/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs113470661). - |
Benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Jul 30, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 01, 2017 | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2021 | This variant is associated with the following publications: (PMID: 24875298, 25262649, 24616153, 12736868) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | MYO1A: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at