rs79255460
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000261.2(MYOC):c.731-73C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 1,537,068 control chromosomes in the GnomAD database, including 682 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 0.021 ( 56 hom., cov: 32)
Exomes 𝑓: 0.026 ( 626 hom. )
Consequence
MYOC
NM_000261.2 intron
NM_000261.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.401
Genes affected
MYOC (HGNC:7610): (myocilin) MYOC encodes the protein myocilin, which is believed to have a role in cytoskeletal function. MYOC is expressed in many occular tissues, including the trabecular meshwork, and was revealed to be the trabecular meshwork glucocorticoid-inducible response protein (TIGR). The trabecular meshwork is a specialized eye tissue essential in regulating intraocular pressure, and mutations in MYOC have been identified as the cause of hereditary juvenile-onset open-angle glaucoma. [provided by RefSeq, Jul 2008]
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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=-0.85).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0206 (3142/152262) while in subpopulation NFE AF= 0.0299 (2037/68022). AF 95% confidence interval is 0.0289. There are 56 homozygotes in gnomad4. There are 1481 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 56 AD,AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOC | NM_000261.2 | c.731-73C>T | intron_variant | ENST00000037502.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOC | ENST00000037502.11 | c.731-73C>T | intron_variant | 1 | NM_000261.2 | P1 | |||
MYOCOS | ENST00000637303.1 | c.235-1848G>A | intron_variant | 5 | A2 | ||||
MYOC | ENST00000638471.1 | c.*69-73C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0207 AC: 3142AN: 152144Hom.: 56 Cov.: 32
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GnomAD4 exome AF: 0.0264 AC: 36521AN: 1384806Hom.: 626 AF XY: 0.0265 AC XY: 18358AN XY: 692444
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GnomAD4 genome ? AF: 0.0206 AC: 3142AN: 152262Hom.: 56 Cov.: 32 AF XY: 0.0199 AC XY: 1481AN XY: 74454
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ClinVar
Not reported inComputational scores
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Name
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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