rs45440292
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002382.5(MAX):c.*405G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,220,868 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0080 ( 6 hom., cov: 33)
Exomes 𝑓: 0.012 ( 77 hom. )
Consequence
MAX
NM_002382.5 3_prime_UTR
NM_002382.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.91
Genes affected
MAX (HGNC:6913): (MYC associated factor X) The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Mutations of this gene have been reported to be associated with hereditary pheochromocytoma. A pseudogene of this gene is located on the long arm of chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 14-65076071-C-T is Benign according to our data. Variant chr14-65076071-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 313806.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00803 (1223/152246) while in subpopulation NFE AF= 0.013 (884/68008). AF 95% confidence interval is 0.0123. There are 6 homozygotes in gnomad4. There are 572 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1223 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAX | NM_002382.5 | c.*405G>A | 3_prime_UTR_variant | 5/5 | ENST00000358664.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAX | ENST00000358664.9 | c.*405G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_002382.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00805 AC: 1224AN: 152130Hom.: 6 Cov.: 33
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GnomAD4 exome AF: 0.0116 AC: 12429AN: 1068622Hom.: 77 Cov.: 34 AF XY: 0.0115 AC XY: 5813AN XY: 504986
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GnomAD4 genome AF: 0.00803 AC: 1223AN: 152246Hom.: 6 Cov.: 33 AF XY: 0.00768 AC XY: 572AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pheochromocytoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
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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