rs4759043
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005379.4(MYO1A):c.1277C>T(p.Pro426Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00745 in 1,613,766 control chromosomes in the GnomAD database, including 1,297 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.1277C>T | p.Pro426Leu | missense_variant | 15/28 | ENST00000300119.8 | |
MYO1A | NM_001256041.2 | c.1277C>T | p.Pro426Leu | missense_variant | 16/29 | ||
MYO1A | XM_047428876.1 | c.1277C>T | p.Pro426Leu | missense_variant | 16/29 | ||
MYO1A | XM_011538373.3 | c.1277C>T | p.Pro426Leu | missense_variant | 15/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.1277C>T | p.Pro426Leu | missense_variant | 15/28 | 1 | NM_005379.4 | P1 | |
MYO1A | ENST00000442789.6 | c.1277C>T | p.Pro426Leu | missense_variant | 16/29 | 1 | P1 | ||
MYO1A | ENST00000476795.1 | n.174C>T | non_coding_transcript_exon_variant | 1/3 | 5 | ||||
MYO1A | ENST00000554234.5 | c.791C>T | p.Pro264Leu | missense_variant, NMD_transcript_variant | 11/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0122 AC: 1858AN: 152196Hom.: 124 Cov.: 32
GnomAD3 exomes AF: 0.0319 AC: 8006AN: 251034Hom.: 989 AF XY: 0.0235 AC XY: 3190AN XY: 135684
GnomAD4 exome AF: 0.00694 AC: 10138AN: 1461452Hom.: 1162 Cov.: 31 AF XY: 0.00575 AC XY: 4184AN XY: 727054
GnomAD4 genome ? AF: 0.0123 AC: 1879AN: 152314Hom.: 135 Cov.: 32 AF XY: 0.0128 AC XY: 951AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 02, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Pro426Leu in Exon 15 of MYO1A: This variant is not expected to have clinical sig nificance because it has been identified in 15.0% (15/100) of chromosomes from a population in the dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP; rs4 759043). - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 25, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at