13-52072067-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365552.1(NEK5):c.1726A>G(p.Met576Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,610,050 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001365552.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEK5 | NM_001365552.1 | c.1726A>G | p.Met576Val | missense_variant | Exon 20 of 24 | ENST00000684899.1 | NP_001352481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEK5 | ENST00000684899.1 | c.1726A>G | p.Met576Val | missense_variant | Exon 20 of 24 | NM_001365552.1 | ENSP00000509632.1 |
Frequencies
GnomAD3 genomes AF: 0.00251 AC: 382AN: 152228Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00259 AC: 645AN: 248956Hom.: 1 AF XY: 0.00271 AC XY: 365AN XY: 134628
GnomAD4 exome AF: 0.00361 AC: 5257AN: 1457704Hom.: 10 Cov.: 28 AF XY: 0.00357 AC XY: 2591AN XY: 725310
GnomAD4 genome AF: 0.00251 AC: 382AN: 152346Hom.: 2 Cov.: 33 AF XY: 0.00244 AC XY: 182AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
NEK5: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at