chr2-15942066-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PVS1PM2BP6
The NM_005378.6(MYCN):c.2T>C(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005378.6 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYCN | NM_005378.6 | c.2T>C | p.Met1? | start_lost | 2/3 | ENST00000281043.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYCN | ENST00000281043.4 | c.2T>C | p.Met1? | start_lost | 2/3 | 5 | NM_005378.6 | P1 | |
MYCN | ENST00000638417.1 | c.157+1323T>C | intron_variant | 2 | |||||
MYCNOS | ENST00000641534.1 | n.98+86A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461322Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726958
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Feingold syndrome type 1 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Service de Génétique Moléculaire, Hôpital Robert Debré | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.