7-132140816-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020911.2(PLXNA4):c.5226-5C>T 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 0.0000725 in 1,613,870 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.5226-5C>T | 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.5226-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_020911.2 | P1 | |||
PLXNA4 | ENST00000359827.7 | c.5226-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 | ||||
PLXNA4 | ENST00000496550.1 | n.390-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 249878Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135494
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727150
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74340
ClinVar
Submissions by phenotype
PLXNA4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 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