chr9-126614491-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001174147.2(LMX1B):c.42C>T(p.Phe14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,482 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 (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
LMX1B
NM_001174147.2 synonymous
NM_001174147.2 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.0220
Genes affected
LMX1B (HGNC:6654): (LIM homeobox transcription factor 1 beta) This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 9-126614491-C-T is Benign according to our data. Variant chr9-126614491-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2811535.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.022 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LMX1B | NM_001174147.2 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | ENST00000373474.9 | NP_001167618.1 | |
| LMX1B | NM_001174146.2 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | NP_001167617.1 | ||
| LMX1B | NM_002316.4 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | NP_002307.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LMX1B | ENST00000373474.9 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | 1 | NM_001174147.2 | ENSP00000362573 | P4 | |
| LMX1B | ENST00000355497.10 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | 1 | ENSP00000347684 | |||
| LMX1B | ENST00000526117.6 | c.42C>T | p.Phe14= | synonymous_variant | 1/8 | 1 | ENSP00000436930 | A1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1451482Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 721232
GnomAD4 exome
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GnomAD4 genome
GnomAD4 genome
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30
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at