rs372851346
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PVS1_ModeratePM2BS1_Supporting
The ENST00000354589.7(PLEC):c.112+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000059 in 1,610,922 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 Uncertain significance (★).
Frequency
Consequence
ENST00000354589.7 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201378.4 | c.71-5086G>A | intron_variant | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000356346.7 | c.71-5086G>A | intron_variant | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000317 AC: 76AN: 239586Hom.: 0 AF XY: 0.000220 AC XY: 29AN XY: 131686
GnomAD4 exome AF: 0.0000610 AC: 89AN: 1458812Hom.: 0 Cov.: 32 AF XY: 0.0000496 AC XY: 36AN XY: 725800
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 14, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at