16-58494832-T-TA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000394282.8(NDRG4):c.133-117dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 531,574 control chromosomes in the GnomAD database, including 159 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 105 hom., cov: 0)
Exomes 𝑓: 0.19 ( 54 hom. )
Consequence
NDRG4
ENST00000394282.8 intron
ENST00000394282.8 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.525
Genes affected
NDRG4 (HGNC:14466): (NDRG family member 4) This gene is a member of the N-myc downregulated gene family which belongs to the alpha/beta hydrolase superfamily. The protein encoded by this gene is a cytoplasmic protein that is required for cell cycle progression and survival in primary astrocytes and may be involved in the regulation of mitogenic signalling in vascular smooth muscles cells. Alternative splicing results in multiple transcripts encoding different isoforms.[provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 16-58494832-T-TA is Benign according to our data. Variant chr16-58494832-T-TA is described in ClinVar as [Benign]. Clinvar id is 1276866.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001130487.2 | c.133-117dup | intron_variant | ||||
NDRG4 | NM_001363869.2 | c.-281-117dup | intron_variant | ||||
NDRG4 | NM_001378332.1 | c.133-117dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000258187.9 | c.73-117dup | intron_variant | 1 | |||||
NDRG4 | ENST00000394282.8 | c.133-117dup | intron_variant | 1 | |||||
NDRG4 | ENST00000394279.6 | c.73-117dup | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0197 AC: 2663AN: 135008Hom.: 103 Cov.: 0
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GnomAD4 exome AF: 0.187 AC: 74246AN: 396588Hom.: 54 AF XY: 0.186 AC XY: 38614AN XY: 207430
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GnomAD4 genome ? AF: 0.0198 AC: 2673AN: 134986Hom.: 105 Cov.: 0 AF XY: 0.0202 AC XY: 1299AN XY: 64370
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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 | Oct 22, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at