chr10-33180348-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003873.7(NRP1):c.2500G>A(p.Glu834Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,599,308 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E834D) has been classified as Uncertain significance.
Frequency
Consequence
NM_003873.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRP1 | NM_003873.7 | c.2500G>A | p.Glu834Lys | missense_variant | 17/17 | ENST00000374867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRP1 | ENST00000374867.7 | c.2500G>A | p.Glu834Lys | missense_variant | 17/17 | 1 | NM_003873.7 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000776 AC: 118AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000833 AC: 205AN: 246188Hom.: 0 AF XY: 0.000925 AC XY: 123AN XY: 132958
GnomAD4 exome AF: 0.00123 AC: 1776AN: 1447150Hom.: 2 Cov.: 32 AF XY: 0.00121 AC XY: 868AN XY: 716978
GnomAD4 genome ? AF: 0.000776 AC: 118AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.000780 AC XY: 58AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | NRP1: BP4, BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2018 | - - |
NRP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at