chr2-132781955-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207363.3(NCKAP5):c.4856C>T(p.Thr1619Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,612,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207363.3 missense
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.4856C>T | p.Thr1619Met | missense_variant | 14/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.4856C>T | p.Thr1619Met | missense_variant | 14/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.458-32646G>A | intron_variant, non_coding_transcript_variant | |||||||
NCKAP5 | ENST00000409213.5 | c.1093-8061C>T | intron_variant | 5 | |||||
NCKAP5 | ENST00000473859.1 | n.69C>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248348Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134626
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460198Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726126
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.4856C>T (p.T1619M) alteration is located in exon 14 (coding exon 12) of the NCKAP5 gene. This alteration results from a C to T substitution at nucleotide position 4856, causing the threonine (T) at amino acid position 1619 to be replaced by a methionine (M). 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