rs61759824
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_052964.4(CLNK):c.92C>T(p.Pro31Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 1,613,330 control chromosomes in the GnomAD database, including 2,511 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P31S) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLNK | NM_052964.4 | c.92C>T | p.Pro31Leu | missense_variant | 4/19 | ENST00000226951.11 | |
CLNK | XM_011513775.3 | c.137C>T | p.Pro46Leu | missense_variant | 4/19 | ||
CLNK | XM_017007684.2 | c.137C>T | p.Pro46Leu | missense_variant | 4/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLNK | ENST00000226951.11 | c.92C>T | p.Pro31Leu | missense_variant | 4/19 | 1 | NM_052964.4 | P1 | |
CLNK | ENST00000507719.1 | c.-35C>T | 5_prime_UTR_variant | 4/13 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0407 AC: 6190AN: 152116Hom.: 186 Cov.: 32
GnomAD3 exomes AF: 0.0432 AC: 10731AN: 248444Hom.: 321 AF XY: 0.0454 AC XY: 6115AN XY: 134728
GnomAD4 exome AF: 0.0535 AC: 78149AN: 1461096Hom.: 2324 Cov.: 31 AF XY: 0.0538 AC XY: 39134AN XY: 726774
GnomAD4 genome AF: 0.0407 AC: 6190AN: 152234Hom.: 187 Cov.: 32 AF XY: 0.0405 AC XY: 3012AN XY: 74430
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at