chr7-132130578-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020911.2(PLXNA4):c.5590-4G>A 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 0.0000824 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_020911.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA4 | NM_020911.2 | c.5590-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000321063.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA4 | ENST00000321063.9 | c.5590-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_020911.2 | P1 | |||
PLXNA4 | ENST00000359827.7 | c.5590-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152074Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000105 AC: 26AN: 248758Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134978
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461808Hom.: 0 Cov.: 61 AF XY: 0.0000839 AC XY: 61AN XY: 727206
GnomAD4 genome AF: 0.000118 AC: 18AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74394
ClinVar
Submissions by phenotype
PLXNA4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2022 | 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