rs7030919

chr9-126676593-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001174147.2(LMX1B):c.327-14243A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,244 control chromosomes in the GnomAD database, including 5,282 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 0.21 (5282 hom., cov: 33)
• Consequence: LMX1B NM_001174147.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMX1B	NM_001174147.2	c.327-14243A>G		intron_variant		ENST00000373474.9
LMX1B	NM_001174146.2	c.327-14243A>G		intron_variant
LMX1B	NM_002316.4	c.327-14243A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMX1B	ENST00000373474.9	c.327-14243A>G		intron_variant		1	NM_001174147.2	P4
LMX1B	ENST00000355497.10	c.327-14243A>G		intron_variant		1
LMX1B	ENST00000526117.6	c.327-14243A>G		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31807 AN: 152126 Hom.: 5254 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.182

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31878 AN: 152244 Hom.: 5282 Cov.: 33 AF XY: 0.205 AC XY: 15261 AN XY: 74444

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.180

Alfa AF: 0.129 Hom.: 2056

Bravo AF: 0.219

Asia WGS AF: 0.124 AC: 434 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	1.7
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs7030919; hg19: chr9-129438872;