Variant 1-51825312-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001101662.2(NRDC):c.1011A>C(p.Gly337Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 1,597,674 control chromosomes in the GnomAD database, including 207,619 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 ( 17583 hom., cov: 32)

Exomes 𝑓: 0.51 ( 190036 hom. )

Consequence

NRDC
NM_001101662.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.752

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP7

Synonymous conserved (PhyloP=0.752 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 link	c.1011A>C	p.Gly337Gly	synonymous_variant	6/31	ENST00000352171.12	NP_001095132.1	O43847-1Q6UUU9
NRDC	NM_002525.3 link	c.1215A>C	p.Gly405Gly	synonymous_variant	8/33		NP_002516.2	O43847-2Q6UUU9
NRDC	NM_001242361.2 link	c.819A>C	p.Gly273Gly	synonymous_variant	8/33		NP_001229290.1	O43847G3V1R5Q6UUU9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRDC	ENST00000352171.12 link	c.1011A>C	p.Gly337Gly	synonymous_variant	6/31	1	NM_001101662.2	ENSP00000262679.8		O43847-1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70482

AN:

151890

Hom.:

17567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.837

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.485

GnomAD3 exomes

AF:

0.508

AC:

120895

AN:

237774

Hom.:

32420

AF XY:

0.503

AC XY:

64845

AN XY:

128832

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.586

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.828

Gnomad SAS exome

AF:

0.402

Gnomad FIN exome

AF:

0.526

Gnomad NFE exome

AF:

0.497

Gnomad OTH exome

AF:

0.505

GnomAD4 exome

AF:

0.506

AC:

732227

AN:

1445666

Hom.:

190036

Cov.:

AF XY:

0.504

AC XY:

362374

AN XY:

719228

show subpopulations

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.588

Gnomad4 ASJ exome

AF:

0.487

Gnomad4 EAS exome

AF:

0.852

Gnomad4 SAS exome

AF:

0.414

Gnomad4 FIN exome

AF:

0.520

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.506

GnomAD4 genome

AF:

0.464

AC:

70518

AN:

152008

Hom.:

17583

Cov.:

AF XY:

0.465

AC XY:

34579

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.559

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.837

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.530

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.491

Alfa

AF:

0.464

Hom.:

6447

Bravo

AF:

0.461

Asia WGS

AF:

0.614

AC:

2134

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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