rs1888687

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003873.7(NRP1):​c.981+7037G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,144 control chromosomes in the GnomAD database, including 2,798 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 0.18 ( 2798 hom., cov: 33)

Consequence

NRP1
NM_003873.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.800
Variant links:
Genes affected
NRP1 (HGNC:8004): (neuropilin 1) This gene encodes one of two neuropilins, which contain specific protein domains which allow them to participate in several different types of signaling pathways that control cell migration. Neuropilins contain a large N-terminal extracellular domain, made up of complement-binding, coagulation factor V/VIII, and meprin domains. These proteins also contains a short membrane-spanning domain and a small cytoplasmic domain. Neuropilins bind many ligands and various types of co-receptors; they affect cell survival, migration, and attraction. Some of the ligands and co-receptors bound by neuropilins are vascular endothelial growth factor (VEGF) and semaphorin family members. 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, Nov 2020]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NRP1NM_003873.7 linkuse as main transcriptc.981+7037G>C intron_variant ENST00000374867.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRP1ENST00000374867.7 linkuse as main transcriptc.981+7037G>C intron_variant 1 NM_003873.7 P3O14786-1

Frequencies

GnomAD3 genomes
AF:
0.176
AC:
26794
AN:
152026
Hom.:
2794
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.260
Gnomad AMR
AF:
0.153
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.514
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.129
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.139
Gnomad OTH
AF:
0.163
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.176
AC:
26829
AN:
152144
Hom.:
2798
Cov.:
33
AF XY:
0.178
AC XY:
13223
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.216
Gnomad4 AMR
AF:
0.153
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.514
Gnomad4 SAS
AF:
0.198
Gnomad4 FIN
AF:
0.129
Gnomad4 NFE
AF:
0.139
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.156
Hom.:
246
Bravo
AF:
0.183
Asia WGS
AF:
0.330
AC:
1145
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.57
DANN
Benign
0.45

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1888687; hg19: chr10-33535919; API