10-102114915-C-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000361198.9(LDB1):c.-593G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 876,016 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000083 ( 0 hom. )
Consequence
LDB1
ENST00000361198.9 5_prime_UTR
ENST00000361198.9 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.989
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BS2
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDB1 | NM_001113407.3 | c.26-3379G>A | intron_variant | ENST00000673968.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDB1 | ENST00000361198.9 | c.-593G>A | 5_prime_UTR_variant | 1/11 | 1 | A1 | |||
LDB1 | ENST00000673968.1 | c.26-3379G>A | intron_variant | NM_001113407.3 | P4 | ||||
LDB1 | ENST00000425280.2 | c.26-3379G>A | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151518Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000828 AC: 6AN: 724384Hom.: 0 Cov.: 10 AF XY: 0.00000594 AC XY: 2AN XY: 336732
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GnomAD4 genome AF: 0.0000198 AC: 3AN: 151632Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74102
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at