chr14-75084618-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_033116.6(NEK9):c.2886A>C(p.Leu962Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,188 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 15 hom. )
Consequence
NEK9
NM_033116.6 missense
NM_033116.6 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 1.43
Genes affected
NEK9 (HGNC:18591): (NIMA related kinase 9) This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein is activated in mitosis and, in turn, activates other family members during mitosis. This protein also mediates cellular processes that are essential for interphase progression. [provided by RefSeq, Jul 2016]
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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=0.005352944).
BP6
?
Variant 14-75084618-T-G is Benign according to our data. Variant chr14-75084618-T-G is described in ClinVar as [Benign]. Clinvar id is 710039.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00995 (1516/152326) while in subpopulation AFR AF= 0.032 (1330/41558). AF 95% confidence interval is 0.0306. There are 20 homozygotes in gnomad4. There are 681 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK9 | NM_033116.6 | c.2886A>C | p.Leu962Phe | missense_variant | 22/22 | ENST00000238616.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK9 | ENST00000238616.10 | c.2886A>C | p.Leu962Phe | missense_variant | 22/22 | 1 | NM_033116.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00991 AC: 1508AN: 152208Hom.: 20 Cov.: 32
GnomAD3 genomes
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1508
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GnomAD3 exomes AF: 0.00339 AC: 853AN: 251362Hom.: 5 AF XY: 0.00265 AC XY: 360AN XY: 135866
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GnomAD4 exome AF: 0.00140 AC: 2053AN: 1461862Hom.: 15 Cov.: 38 AF XY: 0.00141 AC XY: 1025AN XY: 727234
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GnomAD4 genome ? AF: 0.00995 AC: 1516AN: 152326Hom.: 20 Cov.: 32 AF XY: 0.00914 AC XY: 681AN XY: 74484
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ESP6500AA
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156
ESP6500EA
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9
ExAC
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482
Asia WGS
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3
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3478
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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 | Dec 31, 2019 | - - |
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
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
T
Polyphen
P
Vest4
MutPred
Loss of stability (P = 0.1069);
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