3-46603419-T-G

Variant names:

• chr3-46603419-T-G
• rs6799581
• ENST00000505797.1:n.*194+6783T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505797.1(ENSG00000283877):​n.*194+6783T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,962 control chromosomes in the GnomAD database, including 4,429 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 0.24 (4429 hom., cov: 32)
• Consequence: ENSG00000283877 ENST00000505797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

ENSG00000283877 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283877	ENST00000505797.1	n.*194+6783T>G		intron_variant	Intron 3 of 3	3		ENSP00000490854.1
LRRC2	ENST00000682605.1	c.-20+3390A>C		intron_variant	Intron 1 of 8			ENSP00000507018.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36369 AN: 151842 Hom.: 4422 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.239 AC: 36393 AN: 151962 Hom.: 4429 Cov.: 32 AF XY: 0.233 AC XY: 17346 AN XY: 74308

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.275

Alfa AF: 0.259 Hom.: 10594

Bravo AF: 0.252

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6799581; hg19: chr3-46644909;