chr2-182934830-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_013436.5(NCKAP1):c.2781C>G(p.Val927=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 1,424,956 control chromosomes in the GnomAD database, including 430,417 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_013436.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP1 | NM_013436.5 | c.2781C>G | p.Val927= | splice_region_variant, synonymous_variant | 26/31 | ENST00000361354.9 | |
NCKAP1 | NM_205842.3 | c.2799C>G | p.Val933= | splice_region_variant, synonymous_variant | 27/32 | ||
NCKAP1 | XM_006712200.4 | c.2793C>G | p.Val931= | splice_region_variant, synonymous_variant | 27/32 | ||
NCKAP1 | XM_006712201.4 | c.2775C>G | p.Val925= | splice_region_variant, synonymous_variant | 26/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP1 | ENST00000361354.9 | c.2781C>G | p.Val927= | splice_region_variant, synonymous_variant | 26/31 | 1 | NM_013436.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.673 AC: 102225AN: 151942Hom.: 37667 Cov.: 32
GnomAD3 exomes AF: 0.782 AC: 171399AN: 219312Hom.: 68830 AF XY: 0.789 AC XY: 93611AN XY: 118632
GnomAD4 exome AF: 0.780 AC: 992663AN: 1272896Hom.: 392737 Cov.: 20 AF XY: 0.783 AC XY: 500696AN XY: 639436
GnomAD4 genome ? AF: 0.673 AC: 102272AN: 152060Hom.: 37680 Cov.: 32 AF XY: 0.681 AC XY: 50635AN XY: 74362
ClinVar
Submissions by phenotype
NCKAP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at