9-126614883-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001174147.2(LMX1B):c.139+295G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,188 control chromosomes in the GnomAD database, including 646 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.049 (646 hom., cov: 31)
• Consequence: LMX1B NM_001174147.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.72

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 9-126614883-G-A is Benign according to our data. Variant chr9-126614883-G-A is described in ClinVar as [Benign]. Clinvar id is 1225663.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMX1B	NM_001174147.2	c.139+295G>A		intron_variant		ENST00000373474.9
LMX1B	NM_001174146.2	c.139+295G>A		intron_variant
LMX1B	NM_002316.4	c.139+295G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMX1B	ENST00000373474.9	c.139+295G>A		intron_variant		1	NM_001174147.2	P4
LMX1B	ENST00000355497.10	c.139+295G>A		intron_variant		1
LMX1B	ENST00000526117.6	c.139+295G>A		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7470 AN: 152070 Hom.: 646 Cov.: 31

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0491 AC: 7468 AN: 152188 Hom.: 646 Cov.: 31 AF XY: 0.0512 AC XY: 3810 AN XY: 74398

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.0183

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0543

Alfa AF: 0.0354 Hom.: 24

Bravo AF: 0.0601

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.79

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: rs75894916; hg19: chr9-129377162;