rs2903960
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_052964.4(CLNK):c.1083A>T(p.Ile361=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. I361I) has been classified as Benign.
Frequency
Consequence
NM_052964.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLNK | NM_052964.4 | c.1083A>T | p.Ile361= | synonymous_variant | 18/19 | ENST00000226951.11 | |
LOC105374482 | XR_925387.4 | n.261+4758T>A | intron_variant, non_coding_transcript_variant | ||||
CLNK | XM_011513775.3 | c.1128A>T | p.Ile376= | synonymous_variant | 18/19 | ||
CLNK | XM_017007684.2 | c.1128A>T | p.Ile376= | synonymous_variant | 18/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLNK | ENST00000226951.11 | c.1083A>T | p.Ile361= | synonymous_variant | 18/19 | 1 | NM_052964.4 | P1 | |
ENST00000663264.1 | n.97-28821T>A | intron_variant, non_coding_transcript_variant | |||||||
CLNK | ENST00000515667.5 | c.297A>T | p.Ile99= | synonymous_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 45
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at