10-33185710-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_003873.7(NRP1):c.2349C>T(p.Gly783=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G783G) has been classified as Likely benign.
Frequency
Consequence
NM_003873.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRP1 | NM_003873.7 | c.2349C>T | p.Gly783= | synonymous_variant | 15/17 | ENST00000374867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRP1 | ENST00000374867.7 | c.2349C>T | p.Gly783= | synonymous_variant | 15/17 | 1 | NM_003873.7 | P3 | |
NRP1 | ENST00000395995.5 | c.2349C>T | p.Gly783= | synonymous_variant | 15/16 | 1 | A2 | ||
NRP1 | ENST00000374875.5 | c.1785C>T | p.Gly595= | synonymous_variant | 14/16 | 1 | |||
NRP1 | ENST00000265371.8 | c.2349C>T | p.Gly783= | synonymous_variant | 16/18 | 5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251338Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135840
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461366Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727016
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
NRP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 05, 2023 | 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