chr16-58494832-TAAAAAAAAAAA-T

Variant names:

• chr16-58494832-TAAAAAAAAAAA-T
• rs59711785
• ENST00000394282.8:c.133-131_133-121delAAAAAAAAAAA

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 0 publications found

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

ACMG classification

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDRG4	NM_001378332.1		c.133-127_133-117delAAAAAAAAAAA		intron	N/A	NP_001365261.1
	NDRG4	NM_001378333.1		c.133-127_133-117delAAAAAAAAAAA		intron	N/A	NP_001365262.1
	NDRG4	NM_001378334.1		c.133-127_133-117delAAAAAAAAAAA		intron	N/A	NP_001365263.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDRG4	ENST00000394282.8	TSL:1	c.133-131_133-121delAAAAAAAAAAA		intron	N/A	ENSP00000377823.4	Q9ULP0-6
	NDRG4	ENST00000258187.9	TSL:1	c.73-131_73-121delAAAAAAAAAAA		intron	N/A	ENSP00000258187.5	Q9ULP0-3
	NDRG4	ENST00000394279.6	TSL:5	c.73-131_73-121delAAAAAAAAAAA		intron	N/A	ENSP00000377820.2	Q9ULP0-3

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

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

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

Other links and lift over

dbSNP: rs59711785; hg19: chr16-58528736;