chr16-58495135-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000394282.8(NDRG4):c.177+127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00184 in 913,930 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0067 ( 14 hom., cov: 32)
Exomes 𝑓: 0.00087 ( 11 hom. )
Consequence
NDRG4
ENST00000394282.8 intron
ENST00000394282.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.539
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 16-58495135-G-A is Benign according to our data. Variant chr16-58495135-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1317218.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0067 (1020/152304) while in subpopulation AFR AF= 0.0228 (949/41560). AF 95% confidence interval is 0.0216. There are 14 homozygotes in gnomad4. There are 477 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001130487.2 | c.177+127G>A | intron_variant | ||||
NDRG4 | NM_001363869.2 | c.-237+127G>A | intron_variant | ||||
NDRG4 | NM_001378332.1 | c.177+127G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000258187.9 | c.117+127G>A | intron_variant | 1 | |||||
NDRG4 | ENST00000394282.8 | c.177+127G>A | intron_variant | 1 | |||||
NDRG4 | ENST00000394279.6 | c.117+127G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00668 AC: 1017AN: 152186Hom.: 15 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1017
AN:
152186
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.000869 AC: 662AN: 761626Hom.: 11 AF XY: 0.000707 AC XY: 276AN XY: 390450
GnomAD4 exome
AF:
AC:
662
AN:
761626
Hom.:
AF XY:
AC XY:
276
AN XY:
390450
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00670 AC: 1020AN: 152304Hom.: 14 Cov.: 32 AF XY: 0.00641 AC XY: 477AN XY: 74470
GnomAD4 genome
?
AF:
AC:
1020
AN:
152304
Hom.:
Cov.:
32
AF XY:
AC XY:
477
AN XY:
74470
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:
3
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 | Jun 12, 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