rs1046399
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001113407.3(LDB1):c.*459C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 156,832 control chromosomes in the GnomAD database, including 1,745 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.095 ( 1742 hom., cov: 31)
Exomes 𝑓: 0.020 ( 3 hom. )
Consequence
LDB1
NM_001113407.3 3_prime_UTR
NM_001113407.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.68
Genes affected
LDB1 (HGNC:6532): (LIM domain binding 1) Enables LIM domain binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and enzyme binding activity. Involved in negative regulation of transcription, DNA-templated and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDB1 | NM_001113407.3 | c.*459C>T | 3_prime_UTR_variant | 11/11 | ENST00000673968.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDB1 | ENST00000673968.1 | c.*459C>T | 3_prime_UTR_variant | 11/11 | NM_001113407.3 | P4 | |||
LDB1 | ENST00000361198.9 | c.*459C>T | 3_prime_UTR_variant | 11/11 | 1 | A1 | |||
LDB1 | ENST00000425280.2 | c.*459C>T | 3_prime_UTR_variant | 11/11 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0950 AC: 14432AN: 151904Hom.: 1738 Cov.: 31
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GnomAD4 exome AF: 0.0195 AC: 94AN: 4812Hom.: 3 Cov.: 0 AF XY: 0.0200 AC XY: 50AN XY: 2496
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GnomAD4 genome ? AF: 0.0951 AC: 14451AN: 152020Hom.: 1742 Cov.: 31 AF XY: 0.0908 AC XY: 6752AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at