chr4-10501312-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP3BP4_ModerateBP6_ModerateBS2
The NM_052964.4(CLNK):c.1084C>T(p.Arg362Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00203 in 1,607,184 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R362H) has been classified as Uncertain significance.
Frequency
Consequence
NM_052964.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLNK | NM_052964.4 | c.1084C>T | p.Arg362Cys | missense_variant | 18/19 | ENST00000226951.11 | |
LOC105374482 | XR_925387.4 | n.261+4757G>A | intron_variant, non_coding_transcript_variant | ||||
CLNK | XM_011513775.3 | c.1129C>T | p.Arg377Cys | missense_variant | 18/19 | ||
CLNK | XM_017007684.2 | c.1129C>T | p.Arg377Cys | missense_variant | 18/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLNK | ENST00000226951.11 | c.1084C>T | p.Arg362Cys | missense_variant | 18/19 | 1 | NM_052964.4 | P1 | |
ENST00000663264.1 | n.97-28822G>A | intron_variant, non_coding_transcript_variant | |||||||
CLNK | ENST00000515667.5 | c.298C>T | p.Arg100Cys | missense_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00113 AC: 172AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000940 AC: 228AN: 242428Hom.: 1 AF XY: 0.00105 AC XY: 138AN XY: 131840
GnomAD4 exome AF: 0.00213 AC: 3092AN: 1454908Hom.: 4 Cov.: 30 AF XY: 0.00199 AC XY: 1439AN XY: 723714
GnomAD4 genome AF: 0.00113 AC: 172AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.00109 AC XY: 81AN XY: 74448
ClinVar
Submissions by phenotype
CLNK-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 10, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at