rs2241153

Variant names:

• chr2-205771399-C-A
• rs2241153
• NM_003872.3:c.2425+4596C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-205771399-C-A
• chr2-205771399-C-G
• chr2-205771399-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003872.3(NRP2):​c.2425+4596C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,106 control chromosomes in the GnomAD database, including 9,343 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 (9343 hom., cov: 33)
• Consequence: NRP2 NM_003872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRP2	NM_003872.3	c.2425+4596C>A		intron_variant	Intron 15 of 16	ENST00000357785.10	NP_003863.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRP2	ENST00000357785.10	c.2425+4596C>A		intron_variant	Intron 15 of 16	1	NM_003872.3	ENSP00000350432.5

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51752 AN: 151988 Hom.: 9348 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.340 AC: 51761 AN: 152106 Hom.: 9343 Cov.: 33 AF XY: 0.337 AC XY: 25069 AN XY: 74340

African (AFR) AF: 0.229 AC: 9497 AN: 41514

American (AMR) AF: 0.376 AC: 5753 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1573 AN: 5166

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3946 AN: 10578

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27723 AN: 67970

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.380 Hom.: 20067

Bravo AF: 0.339

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2241153; hg19: chr2-206636123;