12-14567623-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024829.6(PLBD1):āc.74T>Cā(p.Leu25Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_024829.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.74T>C | p.Leu25Pro | missense_variant | Exon 1 of 11 | 1 | NM_024829.6 | ENSP00000240617.5 | ||
PLBD1 | ENST00000541618.1 | n.74T>C | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | ENSP00000441278.1 | ||||
PLBD1-AS1 | ENST00000542401.2 | n.231A>G | non_coding_transcript_exon_variant | Exon 1 of 5 | 4 | |||||
PLBD1-AS1 | ENST00000660979.1 | n.162A>G | non_coding_transcript_exon_variant | Exon 1 of 4 |
Frequencies
GnomAD3 genomes AF: 0.00161 AC: 30AN: 18640Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000353 AC: 2AN: 56624Hom.: 0 AF XY: 0.0000605 AC XY: 2AN XY: 33078
GnomAD4 exome AF: 0.000128 AC: 21AN: 163834Hom.: 0 Cov.: 0 AF XY: 0.000142 AC XY: 11AN XY: 77628
GnomAD4 genome AF: 0.00160 AC: 30AN: 18692Hom.: 0 Cov.: 0 AF XY: 0.00142 AC XY: 13AN XY: 9156
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at