rs397517217
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007078.3(LDB3):c.1586C>G(p.Pro529Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P529P) has been classified as Likely benign.
Frequency
Consequence
NM_007078.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDB3 | NM_007078.3 | c.1586C>G | p.Pro529Arg | missense_variant | 10/14 | ENST00000361373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDB3 | ENST00000361373.9 | c.1586C>G | p.Pro529Arg | missense_variant | 10/14 | 1 | NM_007078.3 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461696Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 727168
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 10, 2012 | Variant classified as Uncertain Significance - Favor Benign. The Pro529Arg varia nt (LDB3) has not been reported in the literature nor previously identified by o ur laboratory. Proline (Pro) at position 529 is not conserved in mammals or lowe r species, increasing the likelihood that a change would be tolerated. Computati onal tools are mixed in their prediction on the impact to the protein (AlignGVGD = benign, PolyPhen2 & SIFT = pathogenic), though the accuracy of these tools is unknown. The lack of conservation of this residue suggests that the Pro529Arg v ariant may be benign, but additional information is needed to fully assess its c linical significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at