chr5-16670956-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012334.3(MYO10):c.5453G>T(p.Gly1818Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MYO10
NM_012334.3 missense
NM_012334.3 missense
Scores
8
6
2
Clinical Significance
Conservation
PhyloP100: 4.98
Genes affected
MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.835
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO10 | NM_012334.3 | c.5453G>T | p.Gly1818Val | missense_variant | 39/41 | ENST00000513610.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO10 | ENST00000513610.6 | c.5453G>T | p.Gly1818Val | missense_variant | 39/41 | 1 | NM_012334.3 | P1 | |
RETREG1-AS1 | ENST00000653650.1 | n.330-7878C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247934Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134518
GnomAD3 exomes
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6
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247934
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AN XY:
134518
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000411 AC: 6AN: 1458134Hom.: 0 Cov.: 34 AF XY: 0.00000414 AC XY: 3AN XY: 724546
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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6
AN:
1458134
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Cov.:
34
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3
AN XY:
724546
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ExAC
?
AF:
AC:
2
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.5453G>T (p.G1818V) alteration is located in exon 39 (coding exon 39) of the MYO10 gene. This alteration results from a G to T substitution at nucleotide position 5453, causing the glycine (G) at amino acid position 1818 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;D;D;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;.;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
REVEL
Pathogenic
Sift4G
Uncertain
D;D;D;D
Polyphen
1.0
.;D;.;.
Vest4
MutPred
0.64
.;Loss of disorder (P = 0.0245);.;.;
MVP
MPC
0.82
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at