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GeneBe

16-58494768-G-A

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.67
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]

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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 GnomAd at 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NDRG4NM_001130487.2 linkuse as main transcriptc.133-196G>A intron_variant
NDRG4NM_001363869.2 linkuse as main transcriptc.-281-196G>A intron_variant
NDRG4NM_001378332.1 linkuse as main transcriptc.133-196G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NDRG4ENST00000258187.9 linkuse as main transcriptc.73-196G>A intron_variant 1 Q9ULP0-3
NDRG4ENST00000394282.8 linkuse as main transcriptc.133-196G>A intron_variant 1 Q9ULP0-6
NDRG4ENST00000394279.6 linkuse as main transcriptc.73-196G>A intron_variant 5 Q9ULP0-3

Frequencies

GnomAD3 genomes
AF:
0.00882
AC:
1327
AN:
150382
Hom.:
12
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00226
Gnomad AMI
AF:
0.00220
Gnomad AMR
AF:
0.0111
Gnomad ASJ
AF:
0.00923
Gnomad EAS
AF:
0.0125
Gnomad SAS
AF:
0.00524
Gnomad FIN
AF:
0.0158
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.0113
Gnomad OTH
AF:
0.00725
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00890
AC:
1339
AN:
150502
Hom.:
15
Cov.:
31
AF XY:
0.00910
AC XY:
667
AN XY:
73324
show subpopulations
Gnomad4 AFR
AF:
0.00245
Gnomad4 AMR
AF:
0.0111
Gnomad4 ASJ
AF:
0.00923
Gnomad4 EAS
AF:
0.0130
Gnomad4 SAS
AF:
0.00524
Gnomad4 FIN
AF:
0.0158
Gnomad4 NFE
AF:
0.0113
Gnomad4 OTH
AF:
0.00861
Alfa
AF:
0.0129
Hom.:
2
Bravo
AF:
0.00833
Asia WGS
AF:
0.0200
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 submitterclinical testingGeneDxNov 29, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.72
Dann
Benign
0.61

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs113878610; hg19: chr16-58528672; API