rs754704023
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_007078.3(LDB3):c.689+3861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,742 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_007078.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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LDB3 | ENST00000361373.9 | c.689+3861C>T | intron_variant | Intron 5 of 13 | 1 | NM_007078.3 | ENSP00000355296.3 | |||
LDB3 | ENST00000263066.11 | c.322-14C>T | intron_variant | Intron 4 of 8 | 1 | NM_001368067.1 | ENSP00000263066.7 | |||
ENSG00000289258 | ENST00000443292.2 | c.2198+3861C>T | intron_variant | Intron 15 of 17 | 1 | ENSP00000393132.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000962 AC: 24AN: 249542Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135400
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461536Hom.: 1 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 727094
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
Myofibrillar myopathy 4 Uncertain:1Benign:1
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not specified Benign:2
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c.322-14C>T in intron 3 of LDB3: This variant is not expected to have clinical s ignificance because a C>T change at this position does not diverge from the spli ce consensus sequence and is therefore unlikely to impact splicing. It has been identified in 16/66740 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs754704023). -
not provided Benign:2
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Myofibrillar Myopathy, Dominant Uncertain:1
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Dilated Cardiomyopathy, Dominant Uncertain:1
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Left ventricular noncompaction cardiomyopathy Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at