chr2-132773818-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207363.3(NCKAP5):c.5126T>C(p.Ile1709Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000056 in 1,608,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1709M) has been classified as Uncertain significance.
Frequency
Consequence
NM_207363.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5126T>C | p.Ile1709Thr | missense_variant, splice_region_variant | 16/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5126T>C | p.Ile1709Thr | missense_variant, splice_region_variant | 16/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.458-40783A>G | intron_variant, non_coding_transcript_variant | |||||||
NCKAP5 | ENST00000409213.5 | c.1169T>C | p.Ile390Thr | missense_variant, splice_region_variant | 14/18 | 5 | |||
NCKAP5 | ENST00000473859.1 | n.262+7234T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243076Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131834
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455802Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 724076
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.5126T>C (p.I1709T) alteration is located in exon 16 (coding exon 14) of the NCKAP5 gene. This alteration results from a T to C substitution at nucleotide position 5126, causing the isoleucine (I) at amino acid position 1709 to be replaced by a threonine (T). 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