chr7-37850184-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016616.5(NME8):c.-7-76A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 1,110,362 control chromosomes in the GnomAD database, including 103,026 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 11094 hom., cov: 32)
Exomes 𝑓: 0.43 ( 91932 hom. )
Consequence
NME8
NM_016616.5 intron
NM_016616.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 7-37850184-A-G is Benign according to our data. Variant chr7-37850184-A-G is described in ClinVar as [Benign]. Clinvar id is 1248020.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NME8 | NM_016616.5 | c.-7-76A>G | intron_variant | ENST00000199447.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NME8 | ENST00000199447.9 | c.-7-76A>G | intron_variant | 1 | NM_016616.5 | P1 | |||
NME8 | ENST00000440017.5 | c.-7-76A>G | intron_variant | 1 | P1 | ||||
NME8 | ENST00000444718.5 | c.-7-76A>G | intron_variant | 3 | |||||
NME8 | ENST00000455500.5 | c.-7-76A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.356 AC: 54062AN: 151986Hom.: 11095 Cov.: 32
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GnomAD4 exome AF: 0.432 AC: 413802AN: 958256Hom.: 91932 AF XY: 0.434 AC XY: 216685AN XY: 498804
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GnomAD4 genome AF: 0.355 AC: 54065AN: 152106Hom.: 11094 Cov.: 32 AF XY: 0.358 AC XY: 26593AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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