chr2-182935373-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_013436.5(NCKAP1):c.2698G>A(p.Val900Ile) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013436.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP1 | NM_013436.5 | c.2698G>A | p.Val900Ile | missense_variant, splice_region_variant | 25/31 | ENST00000361354.9 | |
NCKAP1 | NM_205842.3 | c.2716G>A | p.Val906Ile | missense_variant, splice_region_variant | 26/32 | ||
NCKAP1 | XM_006712200.4 | c.2710G>A | p.Val904Ile | missense_variant, splice_region_variant | 26/32 | ||
NCKAP1 | XM_006712201.4 | c.2692G>A | p.Val898Ile | missense_variant, splice_region_variant | 25/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP1 | ENST00000361354.9 | c.2698G>A | p.Val900Ile | missense_variant, splice_region_variant | 25/31 | 1 | NM_013436.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 25
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 26, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.