rs565765056
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_000302.4(PLOD1):c.905C>A(p.Ser302Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,614,088 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000302.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLOD1 | NM_000302.4 | c.905C>A | p.Ser302Tyr | missense_variant | 9/19 | ENST00000196061.5 | |
PLOD1 | NM_001316320.2 | c.1046C>A | p.Ser349Tyr | missense_variant | 10/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLOD1 | ENST00000196061.5 | c.905C>A | p.Ser302Tyr | missense_variant | 9/19 | 1 | NM_000302.4 | P1 | |
PLOD1 | ENST00000465920.1 | n.855C>A | non_coding_transcript_exon_variant | 4/4 | 5 | ||||
PLOD1 | ENST00000485046.5 | n.948C>A | non_coding_transcript_exon_variant | 9/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000450 AC: 113AN: 251184Hom.: 0 AF XY: 0.000589 AC XY: 80AN XY: 135832
GnomAD4 exome AF: 0.000186 AC: 272AN: 1461824Hom.: 3 Cov.: 33 AF XY: 0.000276 AC XY: 201AN XY: 727218
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152264Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 21, 2023 | - - |
Ehlers-Danlos syndrome, kyphoscoliotic type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at