rs75801377
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017433.5(MYO3A):c.3589G>A(p.Glu1197Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 1,614,012 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017433.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO3A | NM_017433.5 | c.3589G>A | p.Glu1197Lys | missense_variant | 30/35 | ENST00000642920.2 | NP_059129.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO3A | ENST00000642920.2 | c.3589G>A | p.Glu1197Lys | missense_variant | 30/35 | NM_017433.5 | ENSP00000495965 | P1 | ||
MYO3A | ENST00000543632.5 | c.1777-37990G>A | intron_variant | 1 | ENSP00000445909 | |||||
MYO3A | ENST00000647478.1 | c.*1393+3314G>A | intron_variant, NMD_transcript_variant | ENSP00000493932 |
Frequencies
GnomAD3 genomes AF: 0.00392 AC: 597AN: 152182Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00107 AC: 268AN: 250560Hom.: 2 AF XY: 0.000723 AC XY: 98AN XY: 135592
GnomAD4 exome AF: 0.000417 AC: 609AN: 1461712Hom.: 7 Cov.: 32 AF XY: 0.000329 AC XY: 239AN XY: 727150
GnomAD4 genome AF: 0.00398 AC: 606AN: 152300Hom.: 5 Cov.: 32 AF XY: 0.00396 AC XY: 295AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | MYO3A: BP4, BS1, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 15, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Glu1197Lys in Exon 30 of MYO3A: This variant is not expected to have clinical si gnificance because it has been identified in 1.1% (41/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs75801377). - |
Autosomal recessive nonsyndromic hearing loss 30 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at