13-77061194-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_015057.5(MYCBP2):āc.13011A>Gā(p.Ala4337=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00039 in 1,608,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.00023 ( 0 hom., cov: 32)
Exomes š: 0.00041 ( 1 hom. )
Consequence
MYCBP2
NM_015057.5 synonymous
NM_015057.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.169
Genes affected
MYCBP2 (HGNC:23386): (MYC binding protein 2) This gene encodes an E3 ubiquitin-protein ligase and member of the PHR (Phr1/MYCBP2, highwire and RPM-1) family of proteins. The encoded protein plays a role in axon guidance and synapse formation in the developing nervous system. In mammalian cells, this protein regulates the cAMP and mTOR signaling pathways, and may additionally regulate autophagy. Reduced expression of this gene has been observed in acute lymphoblastic leukemia patients and a mutation in this gene has been identified in patients with a rare inherited vision defect. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 13-77061194-T-C is Benign according to our data. Variant chr13-77061194-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3055363.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.169 with no splicing effect.
BS2
High AC in GnomAd4 at 35 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYCBP2 | NM_015057.5 | c.13011A>G | p.Ala4337= | synonymous_variant | 76/83 | ENST00000544440.7 | NP_055872.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYCBP2 | ENST00000544440.7 | c.13011A>G | p.Ala4337= | synonymous_variant | 76/83 | 1 | NM_015057.5 | ENSP00000444596 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152168Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000399 AC: 98AN: 245882Hom.: 0 AF XY: 0.000474 AC XY: 63AN XY: 133050
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GnomAD4 exome AF: 0.000406 AC: 592AN: 1456446Hom.: 1 Cov.: 31 AF XY: 0.000399 AC XY: 289AN XY: 724456
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GnomAD4 genome AF: 0.000230 AC: 35AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
MYCBP2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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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