8-127738076-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002467.6(MYC):c.31-172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00989 in 152,260 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0099 ( 25 hom., cov: 33)
Consequence
MYC
NM_002467.6 intron
NM_002467.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.602
Genes affected
MYC (HGNC:7553): (MYC proto-oncogene, bHLH transcription factor) This gene is a proto-oncogene and encodes a nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation. The encoded protein forms a heterodimer with the related transcription factor MAX. This complex binds to the E box DNA consensus sequence and regulates the transcription of specific target genes. Amplification of this gene is frequently observed in numerous human cancers. Translocations involving this gene are associated with Burkitt lymphoma and multiple myeloma in human patients. There is evidence to show that translation initiates both from an upstream, in-frame non-AUG (CUG) and a downstream AUG start site, resulting in the production of two isoforms with distinct N-termini. [provided by RefSeq, Aug 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=-0.8).
BP6
Variant 8-127738076-G-A is Benign according to our data. Variant chr8-127738076-G-A is described in ClinVar as [Benign]. Clinvar id is 2658814.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 1506 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYC | NM_002467.6 | c.31-172G>A | intron_variant | ENST00000621592.8 | NP_002458.2 | |||
MYC | NM_001354870.1 | c.31-175G>A | intron_variant | NP_001341799.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYC | ENST00000621592.8 | c.31-172G>A | intron_variant | 1 | NM_002467.6 | ENSP00000478887 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00990 AC: 1506AN: 152142Hom.: 25 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00989 AC: 1506AN: 152260Hom.: 25 Cov.: 33 AF XY: 0.0108 AC XY: 806AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | CASC11: BS1, BS2; MYC: BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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