2-29920480-C-A
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004304.5(ALK):c.180G>T(p.Val60Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V60V) has been classified as Likely benign.
Frequency
Consequence
NM_004304.5 synonymous
Scores
Clinical Significance
Conservation
Publications
- neuroblastoma, susceptibility to, 3Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALK | ENST00000389048.8 | c.180G>T | p.Val60Val | synonymous_variant | Exon 1 of 29 | 1 | NM_004304.5 | ENSP00000373700.3 | ||
ENSG00000233862 | ENST00000669284.1 | n.157+34769G>T | intron_variant | Intron 1 of 1 | ||||||
ENSG00000233862 | ENST00000769926.1 | n.534+5739G>T | intron_variant | Intron 4 of 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 show subpopulations
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460704Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726646 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74360 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Neuroblastoma, susceptibility to, 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at