chr10-33180368-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003873.7(NRP1):c.2483-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,575,732 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003873.7 splice_region, splice_polypyrimidine_tract, intron
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.2483-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000374867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRP1 | ENST00000374867.7 | c.2483-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003873.7 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00106 AC: 162AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00130 AC: 295AN: 227678Hom.: 0 AF XY: 0.00121 AC XY: 149AN XY: 122808
GnomAD4 exome AF: 0.00136 AC: 1935AN: 1423486Hom.: 2 Cov.: 31 AF XY: 0.00133 AC XY: 934AN XY: 702690
GnomAD4 genome ? AF: 0.00106 AC: 162AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74450
ClinVar
Submissions by phenotype
NRP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 19, 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at