chr16-58487518-TAAAAAAA-T

Variant names:

• chr16-58487518-TAAAAAAA-T
• rs906008307
• ENST00000394282.8:c.38-237_38-231delAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001378332.1(NDRG4):​c.38-230_38-224delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000674 in 148,430 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000067 (0 hom., cov: 34)
• Consequence: NDRG4 NM_001378332.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDRG4	NM_001378332.1	c.38-230_38-224delAAAAAAA		intron_variant	Intron 1 of 17		NP_001365261.1
NDRG4	NM_001378333.1	c.38-230_38-224delAAAAAAA		intron_variant	Intron 1 of 16		NP_001365262.1
NDRG4	NM_001378334.1	c.38-230_38-224delAAAAAAA		intron_variant	Intron 1 of 16		NP_001365263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDRG4	ENST00000394282.8	c.38-237_38-231delAAAAAAA		intron_variant	Intron 1 of 15	1		ENSP00000377823.4
NDRG4	ENST00000258187.9	c.-23-237_-23-231delAAAAAAA		intron_variant	Intron 1 of 15	1		ENSP00000258187.5
NDRG4	ENST00000394279.6	c.-23-237_-23-231delAAAAAAA		intron_variant	Intron 1 of 15	5		ENSP00000377820.2

Frequencies

GnomAD3 genomes AF: 0.00000674 AC: 1 AN: 148430 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000674 AC: 1 AN: 148430 Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 1 AN XY: 72322

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000198

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs906008307; hg19: chr16-58521422;