rs2506140

Variant summary

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

The NM_003873.7(NRP1):​c.*1465T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,178 control chromosomes in the GnomAD database, including 3,123 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 0.19 ( 3123 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

NRP1
NM_003873.7 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NRP1NM_003873.7 linkc.*1465T>C 3_prime_UTR_variant 17/17 ENST00000374867.7 NP_003864.5 O14786-1Q68DN3Q59F20Q6AWA9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NRP1ENST00000374867 linkc.*1465T>C 3_prime_UTR_variant 17/171 NM_003873.7 ENSP00000364001.2 O14786-1
NRP1ENST00000395995 linkc.*1465T>C 3_prime_UTR_variant 16/161 ENSP00000379317.1 E9PEP6
NRP1ENST00000374875 linkc.*1465T>C 3_prime_UTR_variant 16/161 ENSP00000364009.1 Q5JWQ6
NRP1ENST00000265371 linkc.*1465T>C 3_prime_UTR_variant 18/185 ENSP00000265371.3 O14786-1

Frequencies

GnomAD3 genomes
AF:
0.191
AC:
29037
AN:
152060
Hom.:
3114
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.301
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.172
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.131
Gnomad MID
AF:
0.188
Gnomad NFE
AF:
0.156
Gnomad OTH
AF:
0.196
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.191
AC:
29061
AN:
152178
Hom.:
3123
Cov.:
33
AF XY:
0.187
AC XY:
13906
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.301
Gnomad4 AMR
AF:
0.152
Gnomad4 ASJ
AF:
0.172
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.131
Gnomad4 NFE
AF:
0.156
Gnomad4 OTH
AF:
0.197
Alfa
AF:
0.169
Hom.:
2342
Bravo
AF:
0.197
Asia WGS
AF:
0.139
AC:
484
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
12
DANN
Benign
0.75

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: rs2506140; hg19: chr10-33467539; API