9-124013976-AGCAGTGACCGC-A

Variant names:

• chr9-124013976-AGCAGTGACCGC-A
• NM_004789.4:c.139_149delAGTGACCGCGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004789.4(LHX2):​c.139_149delAGTGACCGCGC​(p.Ser47ArgfsTer49) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: LHX2 NM_004789.4 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 10.0

Genes affected

LHX2 (HGNC:6594): (LIM homeobox 2) This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHX2	NM_004789.4	c.139_149delAGTGACCGCGC	p.Ser47ArgfsTer49	frameshift_variant	Exon 2 of 5	ENST00000373615.9	NP_004780.3
LHX2	XM_006717323.4	c.139_149delAGTGACCGCGC	p.Ser47ArgfsTer49	frameshift_variant	Exon 2 of 6		XP_006717386.1
LHX2	XM_047424082.1	c.139_149delAGTGACCGCGC	p.Ser47ArgfsTer49	frameshift_variant	Exon 2 of 6		XP_047280038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHX2	ENST00000373615.9	c.139_149delAGTGACCGCGC	p.Ser47ArgfsTer49	frameshift_variant	Exon 2 of 5	1	NM_004789.4	ENSP00000362717.4
LHX2	ENST00000446480.5	c.130_140delAGTGACCGCGC	p.Ser44ProfsTer87	frameshift_variant	Exon 2 of 5	2		ENSP00000394978.1
LHX2	ENST00000560961.2	c.16_26delAGTGACCGCGC	p.Ser6ArgfsTer49	frameshift_variant	Exon 2 of 3	3		ENSP00000453448.3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Nov 21, 2022

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-126776255;