chr2-132773891-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_207363.3(NCKAP5):āc.5053A>Cā(p.Lys1685Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,609,296 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207363.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5053A>C | p.Lys1685Gln | missense_variant | 16/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5053A>C | p.Lys1685Gln | missense_variant | 16/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.458-40710T>G | intron_variant, non_coding_transcript_variant | |||||||
NCKAP5 | ENST00000409213.5 | c.1096A>C | p.Lys366Gln | missense_variant | 14/18 | 5 | |||
NCKAP5 | ENST00000473859.1 | n.262+7161A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000683 AC: 167AN: 244496Hom.: 0 AF XY: 0.000740 AC XY: 98AN XY: 132458
GnomAD4 exome AF: 0.00136 AC: 1979AN: 1456944Hom.: 2 Cov.: 29 AF XY: 0.00132 AC XY: 955AN XY: 724544
GnomAD4 genome AF: 0.000794 AC: 121AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.5053A>C (p.K1685Q) alteration is located in exon 16 (coding exon 14) of the NCKAP5 gene. This alteration results from a A to C substitution at nucleotide position 5053, causing the lysine (K) at amino acid position 1685 to be replaced by a glutamine (Q). 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