GeneBe

rs7859156

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001174147.2(LMX1B):​c.326+22180T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 25)
Failed GnomAD Quality Control

Consequence

LMX1B
NM_001174147.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571

Publications

4 publications found
Variant links:
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]
LMX1B Gene-Disease associations (from GenCC):
  • nail-patella syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet, G2P
  • nail-patella-like renal disease
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LMX1BNM_001174147.2 linkc.326+22180T>A intron_variant Intron 2 of 7 ENST00000373474.9 NP_001167618.1
LMX1BNM_001174146.2 linkc.326+22180T>A intron_variant Intron 2 of 7 NP_001167617.1
LMX1BNM_002316.4 linkc.326+22180T>A intron_variant Intron 2 of 7 NP_002307.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LMX1BENST00000373474.9 linkc.326+22180T>A intron_variant Intron 2 of 7 1 NM_001174147.2 ENSP00000362573.3
LMX1BENST00000355497.10 linkc.326+22180T>A intron_variant Intron 2 of 7 1 ENSP00000347684.5
LMX1BENST00000526117.6 linkc.326+22180T>A intron_variant Intron 2 of 7 1 ENSP00000436930.1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
150116
Hom.:
0
Cov.:
25
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
150116
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
73054
African (AFR)
AF:
0.00
AC:
0
AN:
40560
American (AMR)
AF:
0.00
AC:
0
AN:
15136
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4988
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4740
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10168
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67758
Other (OTH)
AF:
0.00
AC:
0
AN:
2072

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
6.4
DANN
Benign
0.80
PhyloP100
-0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7859156; hg19: chr9-129400028; API