NM_005378.6:c.-183G>A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005378.6(MYCN):c.-183G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 256,378 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
MYCN
NM_005378.6 5_prime_UTR
NM_005378.6 5_prime_UTR
Scores
6
Clinical Significance
Conservation
PhyloP100: 0.214
Genes affected
MYCN (HGNC:7559): (MYCN proto-oncogene, bHLH transcription factor) This gene is a member of the MYC family and encodes a protein with a basic helix-loop-helix (bHLH) domain. This protein is located in the nucleus and must dimerize with another bHLH protein in order to bind DNA. Amplification of this gene is associated with a variety of tumors, most notably neuroblastomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
MYCNOS (HGNC:16911): (MYCN opposite strand) This gene is transcribed in antisense to the v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog gene (MYCN). It is thought to encode a small, novel protein that stabilizes MYCN, prevents apoptosis, and promotes cell proliferation. Transcripts at this locus may also act directly as functional RNAs to recruit transcriptional regulators to the promoter of MYCN and stimulate transcription of this oncogene. This gene therefore functions through both RNA and protein products. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.14026946).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000137 AC: 2AN: 146320Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000363 AC: 4AN: 110058Hom.: 0 Cov.: 0 AF XY: 0.0000359 AC XY: 2AN XY: 55678
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GnomAD4 genome AF: 0.0000137 AC: 2AN: 146320Hom.: 0 Cov.: 32 AF XY: 0.0000141 AC XY: 1AN XY: 71150
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Feingold syndrome type 1;C5935591:Megalencephaly-polydactyly syndrome Uncertain:1
Aug 26, 2022
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: research
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Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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Benign
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N
LIST_S2
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T
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T
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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