rs35723519

Variant names:

• chr1-51840391-ATCTTCT-A
• rs35723519
• NM_001101662.2:c.459_464delAGAAGA

Your query was ambiguous. Multiple possible variants found:

• chr1-51840391-ATCTTCT-A
• chr1-51840391-ATCTTCT-ATCT
• chr1-51840391-ATCTTCT-ATCTTCTTCT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001101662.2(NRDC):​c.459_464delAGAAGA​(p.Glu153_Glu154del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000456 in 1,536,272 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000043 (0 hom.)
• Consequence: NRDC NM_001101662.2 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.24

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRDC	NM_001101662.2	c.459_464delAGAAGA	p.Glu153_Glu154del	disruptive_inframe_deletion	Exon 2 of 31	ENST00000352171.12	NP_001095132.1
NRDC	NM_002525.3	c.459_464delAGAAGA	p.Glu153_Glu154del	disruptive_inframe_deletion	Exon 2 of 33		NP_002516.2
NRDC	NM_001242361.2	c.63_68delAGAAGA	p.Glu21_Glu22del	disruptive_inframe_deletion	Exon 2 of 33		NP_001229290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRDC	ENST00000352171.12	c.459_464delAGAAGA	p.Glu153_Glu154del	disruptive_inframe_deletion	Exon 2 of 31	1	NM_001101662.2	ENSP00000262679.8

Frequencies

GnomAD3 genomes AF: 0.00000660 AC: 1 AN: 151474 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000433 AC: 6 AN: 1384798 Hom.: 0 AF XY: 0.00000433 AC XY: 3 AN XY: 693112

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000576

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000660 AC: 1 AN: 151474 Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1 AN XY: 73898

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35723519; hg19: chr1-52306063;