rs397517225
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_007078.3(LDB3):c.600C>T(p.Gly200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,636 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G200G) has been classified as Likely benign.
Frequency
Consequence
NM_007078.3 synonymous
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.600C>T | p.Gly200= | synonymous_variant | 5/14 | ENST00000361373.9 | |
LDB3 | NM_001368067.1 | c.321+1557C>T | intron_variant | ENST00000263066.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDB3 | ENST00000361373.9 | c.600C>T | p.Gly200= | synonymous_variant | 5/14 | 1 | NM_007078.3 | P4 | |
LDB3 | ENST00000263066.11 | c.321+1557C>T | intron_variant | 1 | NM_001368067.1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460636Hom.: 0 Cov.: 32 AF XY: 0.00000551 AC XY: 4AN XY: 726470
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 27, 2011 | Gly200Gly in exon 4 of LDB3: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. Gly200Gly in exon 4 of LDB3 (allele frequency = N/A) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at