rs6478750

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001174147.2(LMX1B):​c.326+31350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,108 control chromosomes in the GnomAD database, including 10,325 homozygotes. 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 0.36 ( 10325 hom., cov: 32)

Consequence

LMX1B
NM_001174147.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0860
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LMX1BNM_001174147.2 linkuse as main transcriptc.326+31350T>C intron_variant ENST00000373474.9
LMX1BNM_001174146.2 linkuse as main transcriptc.326+31350T>C intron_variant
LMX1BNM_002316.4 linkuse as main transcriptc.326+31350T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LMX1BENST00000373474.9 linkuse as main transcriptc.326+31350T>C intron_variant 1 NM_001174147.2 P4O60663-1
LMX1BENST00000355497.10 linkuse as main transcriptc.326+31350T>C intron_variant 1 O60663-3
LMX1BENST00000526117.6 linkuse as main transcriptc.326+31350T>C intron_variant 1 A1O60663-2

Frequencies

GnomAD3 genomes
AF:
0.361
AC:
54829
AN:
151990
Hom.:
10311
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.382
Gnomad AMI
AF:
0.314
Gnomad AMR
AF:
0.312
Gnomad ASJ
AF:
0.382
Gnomad EAS
AF:
0.0829
Gnomad SAS
AF:
0.324
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.503
Gnomad NFE
AF:
0.395
Gnomad OTH
AF:
0.365
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.361
AC:
54864
AN:
152108
Hom.:
10325
Cov.:
32
AF XY:
0.354
AC XY:
26344
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.382
Gnomad4 AMR
AF:
0.312
Gnomad4 ASJ
AF:
0.382
Gnomad4 EAS
AF:
0.0835
Gnomad4 SAS
AF:
0.324
Gnomad4 FIN
AF:
0.276
Gnomad4 NFE
AF:
0.395
Gnomad4 OTH
AF:
0.360
Alfa
AF:
0.384
Hom.:
14451
Bravo
AF:
0.360
Asia WGS
AF:
0.200
AC:
694
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
8.0
DANN
Benign
0.59

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6478750; hg19: chr9-129409198; API