10-86716407-A-C
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_007078.3(LDB3):āc.1312A>Cā(p.Thr438Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: š 0.019 ( 0 hom., cov: 0)
Exomes š: 0.00029 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LDB3
NM_007078.3 missense
NM_007078.3 missense
Scores
3
16
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.91
Genes affected
LDB3 (HGNC:15710): (LIM domain binding 3) This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.10600528).
BP6
Variant 10-86716407-A-C is Benign according to our data. Variant chr10-86716407-A-C is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDB3 | NM_007078.3 | c.1312A>C | p.Thr438Pro | missense_variant | 10/14 | ENST00000361373.9 | NP_009009.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDB3 | ENST00000361373.9 | c.1312A>C | p.Thr438Pro | missense_variant | 10/14 | 1 | NM_007078.3 | ENSP00000355296.3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 446AN: 22964Hom.: 0 Cov.: 0 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000286 AC: 247AN: 864694Hom.: 0 Cov.: 34 AF XY: 0.000312 AC XY: 133AN XY: 425884
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0194 AC: 446AN: 22980Hom.: 0 Cov.: 0 AF XY: 0.0195 AC XY: 221AN XY: 11320
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;.;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;M;.
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N
REVEL
Benign
Sift
Benign
D;.;D;T
Sift4G
Benign
T;T;T;T
Polyphen
0.17, 0.12
.;.;B;B
Vest4
MVP
MPC
ClinPred
T
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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