rs886038628
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000199447.9(NME8):āc.594C>Gā(p.Val198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
NME8
ENST00000199447.9 synonymous
ENST00000199447.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0170
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 7-37865590-C-G is Benign according to our data. Variant chr7-37865590-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 260765.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.017 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NME8 | NM_016616.5 | c.594C>G | p.Val198= | synonymous_variant | 10/18 | ENST00000199447.9 | NP_057700.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NME8 | ENST00000199447.9 | c.594C>G | p.Val198= | synonymous_variant | 10/18 | 1 | NM_016616.5 | ENSP00000199447 | P1 | |
NME8 | ENST00000440017.5 | c.594C>G | p.Val198= | synonymous_variant | 9/16 | 1 | ENSP00000397063 | P1 | ||
NME8 | ENST00000444718.5 | c.429C>G | p.Val143= | synonymous_variant | 7/7 | 3 | ENSP00000390596 | |||
NME8 | ENST00000426106.1 | c.105+8245C>G | intron_variant, NMD_transcript_variant | 5 | ENSP00000408841 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460502Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726638
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at