chr2-132731761-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207363.3(NCKAP5):c.5419C>T(p.Arg1807Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00397 in 1,594,324 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 90 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 94 hom. )
Consequence
NCKAP5
NM_207363.3 missense
NM_207363.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.09
Genes affected
NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0016518533).
BP6
?
Variant 2-132731761-G-A is Benign according to our data. Variant chr2-132731761-G-A is described in ClinVar as [Benign]. Clinvar id is 780357.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5419C>T | p.Arg1807Cys | missense_variant | 17/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5419C>T | p.Arg1807Cys | missense_variant | 17/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.457+45296G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0215 AC: 3266AN: 152074Hom.: 88 Cov.: 32
GnomAD3 genomes
?
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3266
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GnomAD3 exomes AF: 0.00519 AC: 1260AN: 242856Hom.: 34 AF XY: 0.00391 AC XY: 515AN XY: 131694
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GnomAD4 exome AF: 0.00212 AC: 3058AN: 1442132Hom.: 94 Cov.: 30 AF XY: 0.00183 AC XY: 1307AN XY: 713854
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GnomAD4 genome ? AF: 0.0215 AC: 3277AN: 152192Hom.: 90 Cov.: 32 AF XY: 0.0210 AC XY: 1563AN XY: 74414
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ESP6500AA
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275
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ExAC
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724
Asia WGS
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14
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;D;D
Polyphen
B;.;.;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at