Variant 1-51798392-A-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.2461T>C(p.Leu821=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,612,772 control chromosomes in the GnomAD database, including 60,235 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 0.34 ( 11023 hom., cov: 31)

Exomes 𝑓: 0.25 ( 49212 hom. )

Consequence

NRDC
NM_001101662.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82

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:

(HGNC:):

links:

OSBPL9 (HGNC:16386): (oxysterol binding protein like 9) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain, although some members contain only the sterol-binding domain. This family member functions as a cholesterol transfer protein that regulates Golgi structure and function. Multiple transcript variants, most of which encode distinct isoforms, have been identified. Related pseudogenes have been identified on chromosomes 3, 11 and 12. [provided by RefSeq, Jul 2010]

OSBPL9 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=-0.34).

BP7

Synonymous conserved (PhyloP=1.82 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NRDC	NM_001101662.2 linkuse as main transcript	c.2461T>C	p.Leu821=	synonymous_variant	22/31	ENST00000352171.12
NRDC	NM_002525.3 linkuse as main transcript	c.2665T>C	p.Leu889=	synonymous_variant	24/33
NRDC	NM_001242361.2 linkuse as main transcript	c.2269T>C	p.Leu757=	synonymous_variant	24/33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRDC	ENST00000352171.12 linkuse as main transcript	c.2461T>C	p.Leu821=	synonymous_variant	22/31	1	NM_001101662.2	P1	O43847-1
	ENST00000586761.2 linkuse as main transcript	n.528A>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51648

AN:

151914

Hom.:

10978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.601

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.334

GnomAD3 exomes

AF:

0.281

AC:

70448

AN:

250928

Hom.:

11592

AF XY:

0.270

AC XY:

36681

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.610

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.185

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.283

GnomAD4 exome

AF:

0.249

AC:

363040

AN:

1460740

Hom.:

49212

Cov.:

AF XY:

0.247

AC XY:

179694

AN XY:

726722

show subpopulations

Gnomad4 AFR exome

AF:

0.618

Gnomad4 AMR exome

AF:

0.406

Gnomad4 ASJ exome

AF:

0.338

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.268

GnomAD4 genome

AF:

0.340

AC:

51738

AN:

152032

Hom.:

11023

Cov.:

AF XY:

0.335

AC XY:

24929

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.602

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.166

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.128

Gnomad4 NFE

AF:

0.236

Gnomad4 OTH

AF:

0.331

Alfa

AF:

0.273

Hom.:

10419

Bravo

AF:

0.373

Asia WGS

AF:

0.244

AC:

850

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.68

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