NM_003872.3:c.1146+3040C>T

Variant names:

• chr2-205731086-C-T
• rs3771033
• NM_003872.3:c.1146+3040C>T

Variant summary

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

The NM_003872.3(NRP2):​c.1146+3040C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,092 control chromosomes in the GnomAD database, including 7,033 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 0.29 (7033 hom., cov: 33)
• Consequence: NRP2 NM_003872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

NRP2 (HGNC:8005): (neuropilin 2) This gene encodes a member of the neuropilin family of receptor proteins. The encoded transmembrane protein binds to SEMA3C protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C} and SEMA3F protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F}, and interacts with vascular endothelial growth factor (VEGF). This protein may play a role in cardiovascular development, axon guidance, and tumorigenesis. This protein has also been determined to act as a co-receptor for SARS-CoV-2 (which causes COVID-19) to infect host cells. [provided by RefSeq, Jul 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRP2	NM_003872.3	c.1146+3040C>T		intron_variant	Intron 7 of 16	ENST00000357785.10	NP_003863.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRP2	ENST00000357785.10	c.1146+3040C>T		intron_variant	Intron 7 of 16	1	NM_003872.3	ENSP00000350432.5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43374 AN: 151972 Hom.: 7022 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.285 AC: 43406 AN: 152092 Hom.: 7033 Cov.: 33 AF XY: 0.293 AC XY: 21799 AN XY: 74354

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.269

Alfa AF: 0.310 Hom.: 7241

Bravo AF: 0.276

Asia WGS AF: 0.399 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.49

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: rs3771033; hg19: chr2-206595810;