NM_024512.5:c.333+2464T>G

Variant names:

• chr3-46542582-A-C
• rs11705987
• NM_024512.5:c.333+2464T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024512.5(LRRC2):​c.333+2464T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,734 control chromosomes in the GnomAD database, including 3,839 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 (3839 hom., cov: 31)
• Consequence: LRRC2 NM_024512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 7 publications found

Genes affected

LRRC2 (HGNC:14676): (leucine rich repeat containing 2) This gene encodes a member of the leucine-rich repeat-containing family of proteins, which function in diverse biological pathways. This family member may possibly be a nuclear protein. Similarity to the RAS suppressor protein, as well as expression down-regulation observed in tumor cells, suggests that it may function as a tumor suppressor. The gene is located in the chromosome 3 common eliminated region 1 (C3CER1), a 1.4 Mb region that is commonly deleted in diverse tumors. A related pseudogene has been identified on chromosome 2. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024512.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC2	NM_024512.5	MANE Select	c.333+2464T>G		intron	N/A	NP_078788.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC2	ENST00000395905.8	TSL:1 MANE Select	c.333+2464T>G		intron	N/A	ENSP00000379241.3
	LRRC2	ENST00000296144.3	TSL:1	c.333+2464T>G		intron	N/A	ENSP00000296144.3
	LRRC2	ENST00000682605.1		c.333+2464T>G		intron	N/A	ENSP00000507018.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31294 AN: 151616 Hom.: 3838 Cov.: 31

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.206 AC: 31305 AN: 151734 Hom.: 3839 Cov.: 31 AF XY: 0.209 AC XY: 15454 AN XY: 74114

African (AFR) AF: 0.0587 AC: 2437 AN: 41512

American (AMR) AF: 0.207 AC: 3154 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3462

East Asian (EAS) AF: 0.192 AC: 991 AN: 5166

South Asian (SAS) AF: 0.285 AC: 1366 AN: 4792

European-Finnish (FIN) AF: 0.309 AC: 3197 AN: 10330

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18443 AN: 67904

Other (OTH) AF: 0.236 AC: 497 AN: 2102

Alfa AF: 0.228 Hom.: 775

Bravo AF: 0.191

Asia WGS AF: 0.225 AC: 780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11705987; hg19: chr3-46584072;