LRRC43 p.Arg330Arg

Variant names:

• chr12-122191465-C-C
• NM_001098519.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr12-122191466--
• chr12-122191466-A-C
• chr12-122191468-G-A
• chr12-122191466-AGG-CGT
• chr12-122191466-AGG-CGC
• chr12-122191466-AGG-CGA

Variant summary

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

The NM_001098519.2(LRRC43):​c. variant causes a intron 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: 31)
• Consequence: LRRC43 NM_001098519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.01
• Publications: 0 publications found

Genes affected

LRRC43 (HGNC:28562): (leucine rich repeat containing 43)

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_001098519.2. 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
	LRRC43	NM_001098519.2	MANE Select	c.		intron	N/A	NP_001091989.1	Q8N309-1
	LRRC43	NM_152759.5		c.		intron	N/A	NP_689972.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC43	ENST00000339777.5	TSL:5 MANE Select	c.		splice_donor intron	N/A	ENSP00000344233.4	Q8N309-1
	LRRC43	ENST00000907479.1		c.		splice_donor intron	N/A	ENSP00000577538.1
	LRRC43	ENST00000541498.5	TSL:5	n.		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.0

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: chr12-122676012;