rs71019410
Positions:
- chr10-86699239-TTCTCTCTCTCTCTC-T
- chr10-86699239-TTCTCTCTCTCTCTC-TTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTC
- chr10-86699239-TTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000361373.9(LDB3):c.896+6684_896+6697del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000102 in 1,563,116 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
LDB3
ENST00000361373.9 intron
ENST00000361373.9 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.30
Genes affected
LDB3 (HGNC:15710): (LIM domain binding 3) This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDB3 | NM_001368067.1 | c.756-23_756-10del | intron_variant | ENST00000263066.11 | NP_001354996.1 | |||
LDB3 | NM_007078.3 | c.896+6684_896+6697del | intron_variant | ENST00000361373.9 | NP_009009.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDB3 | ENST00000263066.11 | c.756-23_756-10del | intron_variant | 1 | NM_001368067.1 | ENSP00000263066 | ||||
LDB3 | ENST00000361373.9 | c.896+6684_896+6697del | intron_variant | 1 | NM_007078.3 | ENSP00000355296 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000672 AC: 1AN: 148748Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
1
AN:
148748
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1414368Hom.: 0 AF XY: 0.0000142 AC XY: 10AN XY: 705986
GnomAD4 exome
AF:
AC:
15
AN:
1414368
Hom.:
AF XY:
AC XY:
10
AN XY:
705986
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000672 AC: 1AN: 148748Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 72356
GnomAD4 genome
AF:
AC:
1
AN:
148748
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
72356
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at