rs55706535
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_004304.5(ALK):c.1390G>T(p.Gly464Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000137 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G464G) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004304.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALK | NM_004304.5 | c.1390G>T | p.Gly464Ter | stop_gained | 6/29 | ENST00000389048.8 | |
LOC101929386 | XR_007086263.1 | n.447+5846C>A | intron_variant, non_coding_transcript_variant | ||||
ALK | XR_001738688.3 | n.2317G>T | non_coding_transcript_exon_variant | 6/18 | |||
LOC101929386 | XR_939920.3 | n.198-11C>A | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALK | ENST00000389048.8 | c.1390G>T | p.Gly464Ter | stop_gained | 6/29 | 1 | NM_004304.5 | P1 | |
ENST00000655343.1 | n.291+5846C>A | intron_variant, non_coding_transcript_variant | |||||||
ALK | ENST00000618119.4 | c.259G>T | p.Gly87Ter | stop_gained | 5/28 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251028Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135672
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at