4-10520803-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052964.4(CLNK):c.760G>A(p.Val254Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052964.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLNK | NM_052964.4 | c.760G>A | p.Val254Met | missense_variant | Exon 15 of 19 | ENST00000226951.11 | NP_443196.2 | |
CLNK | XM_011513775.3 | c.805G>A | p.Val269Met | missense_variant | Exon 15 of 19 | XP_011512077.1 | ||
CLNK | XM_017007684.2 | c.805G>A | p.Val269Met | missense_variant | Exon 15 of 19 | XP_016863173.1 | ||
LOC105374482 | XR_925387.4 | n.262-9327C>T | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1454642Hom.: 0 Cov.: 28 AF XY: 0.00000277 AC XY: 2AN XY: 723232
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.760G>A (p.V254M) alteration is located in exon 15 (coding exon 14) of the CLNK gene. This alteration results from a G to A substitution at nucleotide position 760, causing the valine (V) at amino acid position 254 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at