chr8-127738294-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002467.6(MYC):āc.77A>Gā(p.Asn26Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0319 in 1,610,196 control chromosomes in the GnomAD database, including 1,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002467.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYC | NM_002467.6 | c.77A>G | p.Asn26Ser | missense_variant | 2/3 | ENST00000621592.8 | |
MYC | NM_001354870.1 | c.74A>G | p.Asn25Ser | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYC | ENST00000621592.8 | c.77A>G | p.Asn26Ser | missense_variant | 2/3 | 1 | NM_002467.6 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0240 AC: 3651AN: 152178Hom.: 72 Cov.: 33
GnomAD3 exomes AF: 0.0230 AC: 5750AN: 249536Hom.: 91 AF XY: 0.0231 AC XY: 3117AN XY: 134904
GnomAD4 exome AF: 0.0327 AC: 47736AN: 1457900Hom.: 940 Cov.: 32 AF XY: 0.0318 AC XY: 23053AN XY: 724576
GnomAD4 genome AF: 0.0240 AC: 3648AN: 152296Hom.: 72 Cov.: 33 AF XY: 0.0222 AC XY: 1653AN XY: 74458
ClinVar
Submissions by phenotype
Classic Hodgkin lymphoma Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Pathology Department, Puerta del Mar University Hospital | Oct 01, 2021 | - - |
MYC-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at