GeneBe

rs59711785

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001378332.1(NDRG4):​c.133-127_133-117delAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000024 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

NDRG4
NM_001378332.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.37

Publications

0 publications found
Variant links:
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]
NDRG4 Gene-Disease associations (from GenCC):
  • achromatopsia
    Inheritance: AR Classification: LIMITED Submitted by: G2P

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378332.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NDRG4
NM_001378332.1
c.133-127_133-117delAAAAAAAAAAA
intron
N/ANP_001365261.1
NDRG4
NM_001378333.1
c.133-127_133-117delAAAAAAAAAAA
intron
N/ANP_001365262.1
NDRG4
NM_001378334.1
c.133-127_133-117delAAAAAAAAAAA
intron
N/ANP_001365263.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NDRG4
ENST00000394282.8
TSL:1
c.133-131_133-121delAAAAAAAAAAA
intron
N/AENSP00000377823.4Q9ULP0-6
NDRG4
ENST00000258187.9
TSL:1
c.73-131_73-121delAAAAAAAAAAA
intron
N/AENSP00000258187.5Q9ULP0-3
NDRG4
ENST00000394279.6
TSL:5
c.73-131_73-121delAAAAAAAAAAA
intron
N/AENSP00000377820.2Q9ULP0-3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000244
AC:
1
AN:
409368
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
213998
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
10938
American (AMR)
AF:
0.0000603
AC:
1
AN:
16580
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
11436
East Asian (EAS)
AF:
0.00
AC:
0
AN:
27202
South Asian (SAS)
AF:
0.00
AC:
0
AN:
35316
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24888
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2062
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
258830
Other (OTH)
AF:
0.00
AC:
0
AN:
22116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.725
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs59711785; hg19: chr16-58528736; API