rs779948246
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001174147.2(LMX1B):c.948G>A(p.Gln316=) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
LMX1B
NM_001174147.2 synonymous
NM_001174147.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.96
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 -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 9-126695900-G-A is Benign according to our data. Variant chr9-126695900-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 258632.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMX1B | NM_001174147.2 | c.948G>A | p.Gln316= | synonymous_variant | 7/8 | ENST00000373474.9 | |
LMX1B | NM_001174146.2 | c.981G>A | p.Gln327= | synonymous_variant | 7/8 | ||
LMX1B | NM_002316.4 | c.948G>A | p.Gln316= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMX1B | ENST00000373474.9 | c.948G>A | p.Gln316= | synonymous_variant | 7/8 | 1 | NM_001174147.2 | P4 | |
LMX1B | ENST00000355497.10 | c.981G>A | p.Gln327= | synonymous_variant | 7/8 | 1 | |||
LMX1B | ENST00000526117.6 | c.948G>A | p.Gln316= | synonymous_variant | 7/8 | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247122Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134220
GnomAD3 exomes
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1
AN:
247122
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AN XY:
134220
Gnomad AFR exome
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GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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