chr3-27284640-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001394966.1(NEK10):c.1976A>G(p.Asn659Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00536 in 1,606,922 control chromosomes in the GnomAD database, including 416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 225 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 191 hom. )
Consequence
NEK10
NM_001394966.1 missense
NM_001394966.1 missense
Scores
6
9
Clinical Significance
Conservation
PhyloP100: 4.67
Genes affected
NEK10 (HGNC:18592): (NIMA related kinase 10) Enables protein kinase activity. Involved in several processes, including mucociliary clearance; positive regulation of protein phosphorylation; and regulation of ERK1 and ERK2 cascade. Part of protein kinase complex. Implicated in primary ciliary dyskinesia 44. [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=0.005199492).
BP6
?
Variant 3-27284640-T-C is Benign according to our data. Variant chr3-27284640-T-C is described in ClinVar as [Benign]. Clinvar id is 778065.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK10 | NM_001394966.1 | c.1976A>G | p.Asn659Ser | missense_variant | 22/36 | ENST00000691995.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK10 | ENST00000691995.1 | c.1976A>G | p.Asn659Ser | missense_variant | 22/36 | NM_001394966.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0292 AC: 4435AN: 152140Hom.: 225 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00770 AC: 1935AN: 251388Hom.: 96 AF XY: 0.00570 AC XY: 775AN XY: 135870
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GnomAD4 exome AF: 0.00287 AC: 4181AN: 1454664Hom.: 191 Cov.: 29 AF XY: 0.00250 AC XY: 1812AN XY: 724178
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GnomAD4 genome ? AF: 0.0291 AC: 4438AN: 152258Hom.: 225 Cov.: 32 AF XY: 0.0279 AC XY: 2074AN XY: 74448
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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 | Jul 13, 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;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
P;P;P
PrimateAI
Uncertain
T
Sift4G
Uncertain
T;D
Polyphen
D;.
Vest4
MVP
MPC
0.27
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