rs1553136318
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_000302.4(PLOD1):c.1471-9_1471-8delCCinsGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000302.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLOD1 | NM_000302.4 | c.1471-9_1471-8delCCinsGT | splice_region_variant, intron_variant | Intron 13 of 18 | ENST00000196061.5 | NP_000293.2 | ||
PLOD1 | NM_001316320.2 | c.1612-9_1612-8delCCinsGT | splice_region_variant, intron_variant | Intron 14 of 19 | NP_001303249.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLOD1 | ENST00000196061.5 | c.1471-9_1471-8delCCinsGT | splice_region_variant, intron_variant | Intron 13 of 18 | 1 | NM_000302.4 | ENSP00000196061.4 | |||
PLOD1 | ENST00000470133.1 | n.85-9_85-8delCCinsGT | splice_region_variant, intron_variant | Intron 1 of 2 | 3 | |||||
PLOD1 | ENST00000491536.5 | n.99-9_99-8delCCinsGT | splice_region_variant, intron_variant | Intron 1 of 4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Uncertain:1
PLOD1: PM2, BP4 -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Ehlers-Danlos syndrome, kyphoscoliotic type 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at