LMBRD2 p.Leu20Leu

Variant names:

• chr5-36143289-G-G
• NM_001007527.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr5-36143290--
• chr5-36143292-G-A
• chr5-36143290-C-A
• chr5-36143290-C-G
• chr5-36143290-C-T
• chr5-36143290-CAG-TAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001007527.2(LMBRD2):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LMBRD2 NM_001007527.2 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 0 publications found

Genes affected

LMBRD2 (HGNC:25287): (LMBR1 domain containing 2) Involved in adrenergic receptor signaling pathway. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

LMBRD2 Gene-Disease associations (from GenCC):

• developmental delay with variable neurologic and brain abnormalities

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• neurodevelopmental disorder with microcephaly and dysmorphic facies

  Inheritance: AD Classification: MODERATE Submitted by: Franklin by Genoox
• complex neurodevelopmental disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: Illumina

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007527.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMBRD2	NM_001007527.2	MANE Select	c.		exon_region	Exon 2 of 18	NP_001007528.1	Q68DH5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMBRD2	ENST00000296603.5	TSL:1 MANE Select	c.		exon_region	Exon 2 of 18	ENSP00000296603.4	Q68DH5
	LMBRD2	ENST00000885486.1		c.		exon_region	Exon 2 of 18	ENSP00000555545.1
	LMBRD2	ENST00000885487.1		c.		exon_region	Exon 2 of 18	ENSP00000555546.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr5-36143391;