14-65075349-C-G
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_002382.5(MAX):c.*1127G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,062,706 control chromosomes in the GnomAD database, including 93,923 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.48 ( 20219 hom., cov: 32)
Exomes 𝑓: 0.40 ( 73704 hom. )
Consequence
MAX
NM_002382.5 3_prime_UTR
NM_002382.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.67
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 -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 14-65075349-C-G is Benign according to our data. Variant chr14-65075349-C-G is described in ClinVar as [Benign]. Clinvar id is 313793.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAX | NM_002382.5 | c.*1127G>C | 3_prime_UTR_variant | 5/5 | ENST00000358664.9 | NP_002373.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAX | ENST00000358664 | c.*1127G>C | 3_prime_UTR_variant | 5/5 | 1 | NM_002382.5 | ENSP00000351490.4 |
Frequencies
GnomAD3 genomes AF: 0.481 AC: 73014AN: 151898Hom.: 20175 Cov.: 32
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GnomAD4 exome AF: 0.396 AC: 360992AN: 910690Hom.: 73704 Cov.: 33 AF XY: 0.396 AC XY: 166399AN XY: 420524
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GnomAD4 genome AF: 0.481 AC: 73106AN: 152016Hom.: 20219 Cov.: 32 AF XY: 0.479 AC XY: 35567AN XY: 74278
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pheochromocytoma Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at