7-37850283-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016616.5(NME8):c.17G>A(p.Arg6Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,613,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016616.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NME8 | NM_016616.5 | c.17G>A | p.Arg6Gln | missense_variant | 3/18 | ENST00000199447.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NME8 | ENST00000199447.9 | c.17G>A | p.Arg6Gln | missense_variant | 3/18 | 1 | NM_016616.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152022Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000283 AC: 71AN: 251250Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135774
GnomAD4 exome AF: 0.000109 AC: 160AN: 1461774Hom.: 0 Cov.: 33 AF XY: 0.0000963 AC XY: 70AN XY: 727208
GnomAD4 genome AF: 0.000217 AC: 33AN: 152022Hom.: 0 Cov.: 33 AF XY: 0.000337 AC XY: 25AN XY: 74240
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 13, 2017 | The p.R6Q variant (also known as c.17G>A), located in coding exon 1 of the NME8 gene, results from a G to A substitution at nucleotide position 17. The arginine at codon 6 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at