rs2242027
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016616.5(NME8):c.1247+25A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,430,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
NME8
NM_016616.5 intron
NM_016616.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
NME8 (HGNC:16473): (NME/NM23 family member 8) This gene encodes a protein with an N-terminal thioredoxin domain and three C-terminal nucleoside diphosphate kinase (NDK) domains, but the NDK domains are thought to be catalytically inactive. The sea urchin ortholog of this gene encodes a component of sperm outer dynein arms, and the protein is implicated in ciliary function. Mutations in this gene are implicated in primary ciliary dyskinesia type 6.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NME8 | NM_016616.5 | c.1247+25A>C | intron_variant | ENST00000199447.9 | NP_057700.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NME8 | ENST00000199447.9 | c.1247+25A>C | intron_variant | 1 | NM_016616.5 | ENSP00000199447 | P1 | |||
NME8 | ENST00000440017.5 | c.1247+25A>C | intron_variant | 1 | ENSP00000397063 | P1 | ||||
NME8 | ENST00000426106.1 | c.*193+25A>C | intron_variant, NMD_transcript_variant | 5 | ENSP00000408841 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151972Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000117 AC: 15AN: 1278508Hom.: 0 Cov.: 18 AF XY: 0.00000775 AC XY: 5AN XY: 645312
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74228
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at