Variant rs8375 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001101662.2(NRDC):c.2427C>T(p.Pro809Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,612,516 control chromosomes in the GnomAD database, including 210,959 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 0.46 ( 17446 hom., cov: 32)

Exomes 𝑓: 0.51 ( 193513 hom. )

Consequence

NRDC
NM_001101662.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.57

Variant links:

Genes affected

NRDC (HGNC:7995): (nardilysin convertase) This gene encodes a zinc-dependent endopeptidase that cleaves peptide substrates at the N-terminus of arginine residues in dibasic moieties and is a member of the peptidase M16 family. This protein interacts with heparin-binding EGF-like growth factor and plays a role in cell migration and proliferation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

NRDC links:

NRDC (HGNC:):

NRDC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-3.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRDC	NM_001101662.2 linkuse as main transcript	c.2427C>T	p.Pro809Pro	synonymous_variant	21/31	ENST00000352171.12	NP_001095132.1	O43847-1Q6UUU9
NRDC	NM_002525.3 linkuse as main transcript	c.2631C>T	p.Pro877Pro	synonymous_variant	23/33		NP_002516.2	O43847-2Q6UUU9
NRDC	NM_001242361.2 linkuse as main transcript	c.2235C>T	p.Pro745Pro	synonymous_variant	23/33		NP_001229290.1	O43847G3V1R5Q6UUU9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRDC	ENST00000352171.12 linkuse as main transcript	c.2427C>T	p.Pro809Pro	synonymous_variant	21/31	1	NM_001101662.2	ENSP00000262679.8		O43847-1

Frequencies

GnomAD3 genomes

AF:

0.460

AC:

69783

AN:

151804

Hom.:

17431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.837

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.513

Gnomad OTH

AF:

0.476

GnomAD3 exomes

AF:

0.517

AC:

129783

AN:

250888

Hom.:

35473

AF XY:

0.511

AC XY:

69282

AN XY:

135596

show subpopulations

Gnomad AFR exome

AF:

0.264

Gnomad AMR exome

AF:

0.599

Gnomad ASJ exome

AF:

0.484

Gnomad EAS exome

AF:

0.833

Gnomad SAS exome

AF:

0.412

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.505

Gnomad OTH exome

AF:

0.512

GnomAD4 exome

AF:

0.508

AC:

742312

AN:

1460594

Hom.:

193513

Cov.:

AF XY:

0.506

AC XY:

367337

AN XY:

726588

show subpopulations

Gnomad4 AFR exome

AF:

0.255

Gnomad4 AMR exome

AF:

0.598

Gnomad4 ASJ exome

AF:

0.491

Gnomad4 EAS exome

AF:

0.854

Gnomad4 SAS exome

AF:

0.417

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.507

Gnomad4 OTH exome

AF:

0.503

GnomAD4 genome

AF:

0.460

AC:

69814

AN:

151922

Hom.:

17446

Cov.:

AF XY:

0.462

AC XY:

34293

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.502

Gnomad4 EAS

AF:

0.837

Gnomad4 SAS

AF:

0.419

Gnomad4 FIN

AF:

0.547

Gnomad4 NFE

AF:

0.513

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.495

Hom.:

18406

Bravo

AF:

0.454

Asia WGS

AF:

0.605

AC:

2102

AN:

3478

EpiCase

AF:

0.510

EpiControl

AF:

0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.2

DANN

Benign

0.51

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over