2-29228996-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004304.5(ALK):c.2703C>T(p.Thr901=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000172 in 1,455,970 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. T901T) has been classified as Likely benign.
Frequency
Consequence
NM_004304.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALK | NM_004304.5 | c.2703C>T | p.Thr901= | synonymous_variant | 16/29 | ENST00000389048.8 | |
ALK | XR_001738688.3 | n.3630C>T | non_coding_transcript_exon_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALK | ENST00000389048.8 | c.2703C>T | p.Thr901= | synonymous_variant | 16/29 | 1 | NM_004304.5 | P1 | |
ALK | ENST00000618119.4 | c.1572C>T | p.Thr524= | synonymous_variant | 15/28 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000160 AC: 2AN: 124840Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251170Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135788
GnomAD4 exome AF: 0.0000173 AC: 23AN: 1331130Hom.: 0 Cov.: 35 AF XY: 0.0000167 AC XY: 11AN XY: 660262
GnomAD4 genome AF: 0.0000160 AC: 2AN: 124840Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 58420
ClinVar
Submissions by phenotype
Neuroblastoma, susceptibility to, 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at