chr3-46542682-A-T

Variant names:

• chr3-46542682-A-T
• rs9810340
• NM_024512.5:c.333+2364T>A

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+2364T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,124 control chromosomes in the GnomAD database, including 7,642 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 0.31 (7642 hom., cov: 32)
• Consequence: LRRC2 NM_024512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC2	NM_024512.5	c.333+2364T>A		intron_variant	Intron 3 of 8	ENST00000395905.8	NP_078788.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC2	ENST00000395905.8	c.333+2364T>A		intron_variant	Intron 3 of 8	1	NM_024512.5	ENSP00000379241.3
LRRC2	ENST00000296144.3	c.333+2364T>A		intron_variant	Intron 3 of 8	1		ENSP00000296144.3
LRRC2	ENST00000682605.1	c.333+2364T>A		intron_variant	Intron 3 of 8			ENSP00000507018.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46580 AN: 152004 Hom.: 7648 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.306 AC: 46569 AN: 152124 Hom.: 7642 Cov.: 32 AF XY: 0.297 AC XY: 22081 AN XY: 74348

African (AFR) AF: 0.243 AC: 10069 AN: 41504

American (AMR) AF: 0.303 AC: 4633 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3472

East Asian (EAS) AF: 0.0295 AC: 153 AN: 5188

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2780 AN: 10568

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25477 AN: 67980

Other (OTH) AF: 0.336 AC: 711 AN: 2116

Alfa AF: 0.333 Hom.: 1064

Bravo AF: 0.309

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		0.33
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: rs9810340; hg19: chr3-46584172;