12-109401139-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001101421.4(MYO1H):c.617C>A(p.Ser206Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001101421.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1H | NM_001101421.4 | c.617C>A | p.Ser206Tyr | missense_variant | Exon 6 of 32 | ENST00000310903.10 | NP_001094891.4 | |
MYO1H | XM_011538223.3 | c.569C>A | p.Ser190Tyr | missense_variant | Exon 7 of 34 | XP_011536525.1 | ||
MYO1H | XM_047428738.1 | c.569C>A | p.Ser190Tyr | missense_variant | Exon 5 of 31 | XP_047284694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1H | ENST00000310903.10 | c.617C>A | p.Ser206Tyr | missense_variant | Exon 6 of 32 | 5 | NM_001101421.4 | ENSP00000439182.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249112Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135124
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461676Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727122
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.569C>A (p.S190Y) alteration is located in exon 5 (coding exon 5) of the MYO1H gene. This alteration results from a C to A substitution at nucleotide position 569, causing the serine (S) at amino acid position 190 to be replaced by a tyrosine (Y). 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