rs12761754
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007078.3(LDB3):āc.1442C>Gā(p.Pro481Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,378 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (ā ).
Frequency
Consequence
NM_007078.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDB3 | NM_007078.3 | c.1442C>G | p.Pro481Arg | missense_variant | 10/14 | ENST00000361373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDB3 | ENST00000361373.9 | c.1442C>G | p.Pro481Arg | missense_variant | 10/14 | 1 | NM_007078.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151452Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000108 AC: 27AN: 249068Hom.: 0 AF XY: 0.0000742 AC XY: 10AN XY: 134852
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461808Hom.: 0 Cov.: 36 AF XY: 0.00000688 AC XY: 5AN XY: 727202
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151570Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74052
ClinVar
Submissions by phenotype
Myofibrillar myopathy 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at