16-58487518-TA-T

Variant names:

• chr16-58487518-TA-T
• rs906008307
• ENST00000394282.8:c.38-237delA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001378332.1(NDRG4):​c.38-224delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000728 in 148,406 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.00073 (0 hom., cov: 34)
• Consequence: NDRG4 NM_001378332.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.420

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 16-58487518-TA-T is Benign according to our data. Variant chr16-58487518-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317111.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDRG4	NM_001378332.1	c.38-224delA		intron_variant	Intron 1 of 17		NP_001365261.1
NDRG4	NM_001378333.1	c.38-224delA		intron_variant	Intron 1 of 16		NP_001365262.1
NDRG4	NM_001378334.1	c.38-224delA		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.38-237delA		intron_variant	Intron 1 of 15	1		ENSP00000377823.4
NDRG4	ENST00000258187.9	c.-23-237delA		intron_variant	Intron 1 of 15	1		ENSP00000258187.5
NDRG4	ENST00000394279.6	c.-23-237delA		intron_variant	Intron 1 of 15	5		ENSP00000377820.2

Frequencies

GnomAD3 genomes AF: 0.000701 AC: 104 AN: 148324 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.000748

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000540

Gnomad ASJ AF: 0.000580

Gnomad EAS AF: 0.000396

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00193

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000642

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000728 AC: 108 AN: 148406 Hom.: 0 Cov.: 34 AF XY: 0.000898 AC XY: 65 AN XY: 72364

Gnomad4 AFR AF: 0.000845

Gnomad4 AMR AF: 0.000539

Gnomad4 ASJ AF: 0.000580

Gnomad4 EAS AF: 0.000397

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00193

Gnomad4 NFE AF: 0.000642

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 22, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;