12-14506992-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024829.6(PLBD1):c.1313G>A(p.Arg438Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,613,944 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 60 hom. )
Consequence
PLBD1
NM_024829.6 missense
NM_024829.6 missense
Scores
6
5
8
Clinical Significance
Conservation
PhyloP100: 7.38
Genes affected
PLBD1 (HGNC:26215): (phospholipase B domain containing 1) Predicted to enable phospholipase activity. Predicted to be involved in phospholipid catabolic process. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.01349023).
BP6
Variant 12-14506992-C-T is Benign according to our data. Variant chr12-14506992-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642755.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLBD1 | NM_024829.6 | c.1313G>A | p.Arg438Gln | missense_variant | 9/11 | ENST00000240617.10 | NP_079105.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.1313G>A | p.Arg438Gln | missense_variant | 9/11 | 1 | NM_024829.6 | ENSP00000240617 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00588 AC: 894AN: 152002Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00612 AC: 1539AN: 251348Hom.: 21 AF XY: 0.00593 AC XY: 806AN XY: 135836
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GnomAD4 exome AF: 0.00489 AC: 7152AN: 1461826Hom.: 60 Cov.: 30 AF XY: 0.00490 AC XY: 3567AN XY: 727222
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GnomAD4 genome AF: 0.00588 AC: 894AN: 152118Hom.: 8 Cov.: 32 AF XY: 0.00573 AC XY: 426AN XY: 74348
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | PLBD1: BP4, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at