rs3750733

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_003873.7(NRP1):c.60C>T(p.Gly20Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 1,542,044 control chromosomes in the GnomAD database, including 7,778 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.080 ( 621 hom., cov: 31)

Exomes 𝑓: 0.095 ( 7157 hom. )

Consequence

NRP1
NM_003873.7 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.58

Publications

10 publications found

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]

NRP1 Gene-Disease associations (from GenCC):

congenital heart disease
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

NRP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 10-33334323-G-A is Benign according to our data. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-33334323-G-A is described in CliVar as Benign. Clinvar id is 3057002.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRP1	NM_003873.7 link	c.60C>T	p.Gly20Gly	synonymous_variant	Exon 1 of 17	ENST00000374867.7	NP_003864.5	O14786-1Q68DN3Q59F20Q6AWA9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRP1	ENST00000374867.7 link	c.60C>T	p.Gly20Gly	synonymous_variant	Exon 1 of 17	1	NM_003873.7	ENSP00000364001.2		O14786-1

Frequencies

GnomAD3 genomes

AF:

0.0798

AC:

12145

AN:

152110

Hom.:

617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0478

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.0900

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.0676

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0837

Gnomad OTH

AF:

0.0808

GnomAD2 exomes

AF:

0.109

AC:

15177

AN:

139364

AF XY:

0.112

show subpopulations

Gnomad AFR exome

AF:

0.0430

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.0586

Gnomad EAS exome

AF:

0.203

Gnomad FIN exome

AF:

0.0632

Gnomad NFE exome

AF:

0.0832

Gnomad OTH exome

AF:

0.0927

GnomAD4 exome

AF:

0.0955

AC:

132685

AN:

1389816

Hom.:

7157

Cov.:

AF XY:

0.0974

AC XY:

66788

AN XY:

685678

show subpopulations

African (AFR)

AF:

0.0430

AC:

1355

AN:

31508

American (AMR)

AF:

0.116

AC:

4146

AN:

35672

Ashkenazi Jewish (ASJ)

AF:

0.0554

AC:

1391

AN:

25128

East Asian (EAS)

AF:

0.197

AC:

6989

AN:

35528

South Asian (SAS)

AF:

0.170

AC:

13439

AN:

78988

European-Finnish (FIN)

AF:

0.0668

AC:

2834

AN:

42414

Middle Eastern (MID)

AF:

0.0642

AC:

311

AN:

4848

European-Non Finnish (NFE)

AF:

0.0895

AC:

96437

AN:

1077932

Other (OTH)

AF:

0.100

AC:

5783

AN:

57798

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

5845

11690

17534

23379

29224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3784

7568

11352

15136

18920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0799

AC:

12159

AN:

152228

Hom.:

621

Cov.:

AF XY:

0.0819

AC XY:

6095

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0477

AC:

1984

AN:

41554

American (AMR)

AF:

0.0907

AC:

1387

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0516

AC:

179

AN:

3468

East Asian (EAS)

AF:

0.211

AC:

1086

AN:

5136

South Asian (SAS)

AF:

0.182

AC:

878

AN:

4826

European-Finnish (FIN)

AF:

0.0676

AC:

717

AN:

10610

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0836

AC:

5689

AN:

68020

Other (OTH)

AF:

0.0818

AC:

173

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

548

1096

1645

2193

2741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0850

Hom.:

523

Bravo

AF:

0.0778

Asia WGS

AF:

0.214

AC:

745

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

NRP1-related disorder

Benign:1

Aug 01, 2022

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.97

PhyloP100

1.6

PromoterAI

-0.019

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Mutation Taster

=297/3

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over