rs1058219
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001382347.1(MYO5A):c.3736C>T(p.Arg1246Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,614,020 control chromosomes in the GnomAD database, including 21,616 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1246H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382347.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.3736C>T | p.Arg1246Cys | missense_variant | 28/42 | ENST00000399233.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO5A | ENST00000399233.7 | c.3736C>T | p.Arg1246Cys | missense_variant | 28/42 | 5 | NM_001382347.1 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22847AN: 152048Hom.: 1816 Cov.: 32
GnomAD3 exomes AF: 0.156 AC: 38829AN: 249556Hom.: 3180 AF XY: 0.156 AC XY: 21155AN XY: 135394
GnomAD4 exome AF: 0.163 AC: 237836AN: 1461854Hom.: 19806 Cov.: 34 AF XY: 0.162 AC XY: 118133AN XY: 727228
GnomAD4 genome ? AF: 0.150 AC: 22838AN: 152166Hom.: 1810 Cov.: 32 AF XY: 0.148 AC XY: 10988AN XY: 74408
ClinVar
Submissions by phenotype
Griscelli syndrome type 1 Benign:2
Benign, no assertion criteria provided | literature only | OMIM | Jul 01, 1997 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at