rs9514923
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001198950.3(MYO16):c.868-6056A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,152 control chromosomes in the GnomAD database, including 59,495 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.86 ( 59495 hom., cov: 32)
Consequence
MYO16
NM_001198950.3 intron
NM_001198950.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.83
Genes affected
MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO16 | NM_001198950.3 | c.868-6056A>G | intron_variant | ENST00000457511.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO16 | ENST00000457511.7 | c.868-6056A>G | intron_variant | 1 | NM_001198950.3 | A2 | |||
MYO16 | ENST00000356711.7 | c.802-6056A>G | intron_variant | 1 | P2 | ||||
MYO16 | ENST00000251041.10 | c.802-6056A>G | intron_variant | 5 | |||||
MYO16 | ENST00000375857.6 | n.188-6056A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.859 AC: 130588AN: 152034Hom.: 59486 Cov.: 32
GnomAD3 genomes
?
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130588
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.859 AC: 130631AN: 152152Hom.: 59495 Cov.: 32 AF XY: 0.862 AC XY: 64156AN XY: 74406
GnomAD4 genome
?
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130631
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152152
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32
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64156
AN XY:
74406
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3265
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3472
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at