chr16-58464080-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000394282.8(NDRG4):c.-351G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 244,438 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.030 ( 103 hom., cov: 32)
Exomes 𝑓: 0.022 ( 35 hom. )
Consequence
NDRG4
ENST00000394282.8 5_prime_UTR
ENST00000394282.8 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.02
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 16-58464080-G-T is Benign according to our data. Variant chr16-58464080-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1316103.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0297 (4514/152090) while in subpopulation AFR AF= 0.0483 (2008/41536). AF 95% confidence interval is 0.0466. There are 103 homozygotes in gnomad4. There are 2160 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 102 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001378338.1 | c.-24+283G>T | intron_variant | ||||
NDRG4 | NM_001378339.1 | c.-24+283G>T | intron_variant | ||||
NDRG4 | NM_001378342.1 | c.-24+283G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000394282.8 | c.-351G>T | 5_prime_UTR_variant | 1/16 | 1 | ||||
NDRG4 | ENST00000258187.9 | c.-24+283G>T | intron_variant | 1 | |||||
NDRG4 | ENST00000564126.5 | c.-24+283G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0296 AC: 4502AN: 151984Hom.: 102 Cov.: 32
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GnomAD4 exome AF: 0.0216 AC: 1993AN: 92348Hom.: 35 Cov.: 0 AF XY: 0.0208 AC XY: 975AN XY: 46788
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GnomAD4 genome ? AF: 0.0297 AC: 4514AN: 152090Hom.: 103 Cov.: 32 AF XY: 0.0290 AC XY: 2160AN XY: 74378
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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 | Apr 16, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at