chr13-108793536-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001198950.3(MYO16):c.637C>T(p.Arg213Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,613,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R213L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001198950.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO16 | NM_001198950.3 | c.637C>T | p.Arg213Cys | missense_variant | 6/35 | ENST00000457511.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO16 | ENST00000457511.7 | c.637C>T | p.Arg213Cys | missense_variant | 6/35 | 1 | NM_001198950.3 | A2 | |
MYO16 | ENST00000356711.7 | c.571C>T | p.Arg191Cys | missense_variant | 6/35 | 1 | P2 | ||
MYO16 | ENST00000251041.10 | c.571C>T | p.Arg191Cys | missense_variant | 6/25 | 5 | |||
MYO16 | ENST00000375857.6 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251384Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135862
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461482Hom.: 1 Cov.: 30 AF XY: 0.0000715 AC XY: 52AN XY: 727062
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.637C>T (p.R213C) alteration is located in exon 6 (coding exon 6) of the MYO16 gene. This alteration results from a C to T substitution at nucleotide position 637, causing the arginine (R) at amino acid position 213 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at