rs2506140
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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
NM_003873.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.29
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRP1 | ENST00000374867 | c.*1465T>C | 3_prime_UTR_variant | 17/17 | 1 | NM_003873.7 | ENSP00000364001.2 | |||
NRP1 | ENST00000395995 | c.*1465T>C | 3_prime_UTR_variant | 16/16 | 1 | ENSP00000379317.1 | ||||
NRP1 | ENST00000374875 | c.*1465T>C | 3_prime_UTR_variant | 16/16 | 1 | ENSP00000364009.1 | ||||
NRP1 | ENST00000265371 | c.*1465T>C | 3_prime_UTR_variant | 18/18 | 5 | ENSP00000265371.3 |
Frequencies
GnomAD3 genomes AF: 0.191 AC: 29037AN: 152060Hom.: 3114 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome AF: 0.191 AC: 29061AN: 152178Hom.: 3123 Cov.: 33 AF XY: 0.187 AC XY: 13906AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at