rs2977499

chr8-133267532-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006096.4(NDRG1):c.100-2880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,084 control chromosomes in the GnomAD database, including 5,548 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5548 hom., cov: 32)
• Consequence: NDRG1 NM_006096.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

Genes affected

NDRG1 (HGNC:7679): (N-myc downstream regulated 1) 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 involved in stress responses, hormone responses, cell growth, and differentiation. The encoded protein is necessary for p53-mediated caspase activation and apoptosis. Mutations in this gene are a cause of Charcot-Marie-Tooth disease type 4D, and expression of this gene may be a prognostic indicator for several types of cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDRG1	NM_006096.4	c.100-2880A>G		intron_variant		ENST00000323851.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDRG1	ENST00000323851.13	c.100-2880A>G		intron_variant		1	NM_006096.4	P1

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39227 AN: 151966 Hom.: 5547 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.258 AC: 39247 AN: 152084 Hom.: 5548 Cov.: 32 AF XY: 0.261 AC XY: 19405 AN XY: 74344

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.262

Alfa AF: 0.279 Hom.: 1004

Bravo AF: 0.256

Asia WGS AF: 0.359 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	21
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2977499; hg19: chr8-134279775;