rs1770791
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001101662.2(NRDC):āc.2461T>Cā(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: š 0.34 ( 11023 hom., cov: 31)
Exomes š: 0.25 ( 49212 hom. )
Consequence
NRDC
NM_001101662.2 synonymous
NM_001101662.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.82
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]
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]
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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 | UniProt |
---|---|---|---|---|---|---|---|
NRDC | NM_001101662.2 | c.2461T>C | p.Leu821= | synonymous_variant | 22/31 | ENST00000352171.12 | |
NRDC | NM_002525.3 | c.2665T>C | p.Leu889= | synonymous_variant | 24/33 | ||
NRDC | NM_001242361.2 | c.2269T>C | p.Leu757= | synonymous_variant | 24/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRDC | ENST00000352171.12 | c.2461T>C | p.Leu821= | synonymous_variant | 22/31 | 1 | NM_001101662.2 | P1 | |
ENST00000586761.2 | n.528A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.340 AC: 51648AN: 151914Hom.: 10978 Cov.: 31
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GnomAD3 exomes AF: 0.281 AC: 70448AN: 250928Hom.: 11592 AF XY: 0.270 AC XY: 36681AN XY: 135628
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GnomAD4 exome AF: 0.249 AC: 363040AN: 1460740Hom.: 49212 Cov.: 32 AF XY: 0.247 AC XY: 179694AN XY: 726722
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GnomAD4 genome ? AF: 0.340 AC: 51738AN: 152032Hom.: 11023 Cov.: 31 AF XY: 0.335 AC XY: 24929AN XY: 74342
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at