chr16-58494768-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000394282.8(NDRG4):c.133-196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0089 in 150,502 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 15 hom., cov: 31)
Consequence
NDRG4
ENST00000394282.8 intron
ENST00000394282.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 16-58494768-G-A is Benign according to our data. Variant chr16-58494768-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316368.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001130487.2 | c.133-196G>A | intron_variant | ||||
NDRG4 | NM_001363869.2 | c.-281-196G>A | intron_variant | ||||
NDRG4 | NM_001378332.1 | c.133-196G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000258187.9 | c.73-196G>A | intron_variant | 1 | |||||
NDRG4 | ENST00000394282.8 | c.133-196G>A | intron_variant | 1 | |||||
NDRG4 | ENST00000394279.6 | c.73-196G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00882 AC: 1327AN: 150382Hom.: 12 Cov.: 31
GnomAD3 genomes
AF:
AC:
1327
AN:
150382
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00890 AC: 1339AN: 150502Hom.: 15 Cov.: 31 AF XY: 0.00910 AC XY: 667AN XY: 73324
GnomAD4 genome
AF:
AC:
1339
AN:
150502
Hom.:
Cov.:
31
AF XY:
AC XY:
667
AN XY:
73324
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
68
AN:
3478
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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at