2-105881433-A-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003581.5(NCK2):c.332A>T(p.Asp111Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003581.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCK2 | NM_003581.5 | c.332A>T | p.Asp111Val | missense_variant | Exon 4 of 5 | ENST00000233154.9 | NP_003572.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250220Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135550
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461088Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 726902
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.332A>T (p.D111V) alteration is located in exon 1 (coding exon 1) of the NCK2 gene. This alteration results from a A to T substitution at nucleotide position 332, causing the aspartic acid (D) at amino acid position 111 to be replaced by a valine (V). 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