rs6828134
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001199397.3(NEK1):āc.2731C>Gā(p.Gln911Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000925 in 1,612,356 control chromosomes in the GnomAD database, including 11 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 Likely benign (ā ā ).
Frequency
Consequence
NM_001199397.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK1 | NM_001199397.3 | c.2731C>G | p.Gln911Glu | missense_variant | 28/36 | ENST00000507142.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK1 | ENST00000507142.6 | c.2731C>G | p.Gln911Glu | missense_variant | 28/36 | 1 | NM_001199397.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00489 AC: 745AN: 152206Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00119 AC: 293AN: 246646Hom.: 2 AF XY: 0.000906 AC XY: 121AN XY: 133626
GnomAD4 exome AF: 0.000511 AC: 746AN: 1460032Hom.: 6 Cov.: 30 AF XY: 0.000461 AC XY: 335AN XY: 726048
GnomAD4 genome AF: 0.00489 AC: 745AN: 152324Hom.: 5 Cov.: 33 AF XY: 0.00454 AC XY: 338AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 27, 2023 | See Variant Classification Assertion Criteria. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 21, 2023 | - - |
Short-rib thoracic dysplasia 6 with or without polydactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at