chr16-58487860-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000394282.8(NDRG4):c.132+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,528,474 control chromosomes in the GnomAD database, including 123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 9 hom., cov: 32)
Exomes 𝑓: 0.011 ( 114 hom. )
Consequence
NDRG4
ENST00000394282.8 intron
ENST00000394282.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0200
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 16-58487860-A-G is Benign according to our data. Variant chr16-58487860-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1316367.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001130487.2 | c.132+10A>G | intron_variant | ||||
NDRG4 | NM_001363869.2 | c.-282+10A>G | intron_variant | ||||
NDRG4 | NM_001378332.1 | c.132+10A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000258187.9 | c.72+10A>G | intron_variant | 1 | |||||
NDRG4 | ENST00000394282.8 | c.132+10A>G | intron_variant | 1 | |||||
NDRG4 | ENST00000394279.6 | c.72+10A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00749 AC: 1140AN: 152126Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00773 AC: 1048AN: 135616Hom.: 4 AF XY: 0.00814 AC XY: 589AN XY: 72374
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GnomAD4 exome AF: 0.0113 AC: 15495AN: 1376230Hom.: 114 Cov.: 30 AF XY: 0.0112 AC XY: 7598AN XY: 676496
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GnomAD4 genome AF: 0.00748 AC: 1139AN: 152244Hom.: 9 Cov.: 32 AF XY: 0.00717 AC XY: 534AN XY: 74438
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 29, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at