chr7-7573222-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_019005.4(MIOS):c.747A>G(p.Ala249=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,614,168 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000098 ( 2 hom. )
Consequence
MIOS
NM_019005.4 synonymous
NM_019005.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.19
Genes affected
MIOS (HGNC:21905): (meiosis regulator for oocyte development) Involved in cellular response to amino acid starvation; positive regulation of TOR signaling; and protein-containing complex localization. Located in several cellular components, including cytosol; lysosomal membrane; and nucleoplasm. Part of GATOR2 complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 7-7573222-A-G is Benign according to our data. Variant chr7-7573222-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 728748.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.19 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIOS | NM_019005.4 | c.747A>G | p.Ala249= | synonymous_variant | 4/13 | ENST00000340080.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIOS | ENST00000340080.9 | c.747A>G | p.Ala249= | synonymous_variant | 4/13 | 1 | NM_019005.4 | P1 | |
MIOS | ENST00000405785.5 | c.747A>G | p.Ala249= | synonymous_variant | 3/12 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000205 AC: 51AN: 249288Hom.: 1 AF XY: 0.000288 AC XY: 39AN XY: 135250
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GnomAD4 exome AF: 0.0000978 AC: 143AN: 1461846Hom.: 2 Cov.: 31 AF XY: 0.000151 AC XY: 110AN XY: 727214
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at