1-51832797-G-T

Position:

• chr1-51832797-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001101662.2(NRDC):​c.866+1220C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,102 control chromosomes in the GnomAD database, including 413 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 0.046 (413 hom., cov: 32)
• Consequence: NRDC NM_001101662.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRDC	NM_001101662.2	c.866+1220C>A		intron_variant		ENST00000352171.12	NP_001095132.1
NRDC	NM_001242361.2	c.674+1220C>A		intron_variant			NP_001229290.1
NRDC	NM_002525.3	c.1070+1220C>A		intron_variant			NP_002516.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRDC	ENST00000352171.12	c.866+1220C>A		intron_variant		1	NM_001101662.2	ENSP00000262679	P1

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7011 AN: 151984 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.000379

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00837

Gnomad OTH AF: 0.0287

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0463 AC: 7037 AN: 152102 Hom.: 413 Cov.: 32 AF XY: 0.0466 AC XY: 3466 AN XY: 74380

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.000379

Gnomad4 NFE AF: 0.00837

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0126 Hom.: 16

Bravo AF: 0.0480

Asia WGS AF: 0.0710 AC: 244 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.28

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

Other links and lift over

dbSNP: rs1417367; hg19: chr1-52298469;