NM_130830.5:c.-3-387delG

Variant names:

• chr3-194361432-TC-T
• rs11313667
• NM_130830.5:c.-3-387delG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_130830.5(LRRC15):​c.-3-387delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (24304 hom., cov: 0)
• Consequence: LRRC15 NM_130830.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 5 publications found

Genes affected

LRRC15 (HGNC:20818): (leucine rich repeat containing 15) Enables collagen binding activity; fibronectin binding activity; and laminin binding activity. Involved in negative regulation of protein localization to plasma membrane; positive regulation of cell migration; and receptor-mediated virion attachment to host cell. Located in extracellular exosome. Colocalizes with collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC15	NM_130830.5	c.-3-387delG		intron_variant	Intron 1 of 1	ENST00000347624.4	NP_570843.2
LRRC15	NM_001135057.3	c.16-387delG		intron_variant	Intron 2 of 2		NP_001128529.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC15	ENST00000347624.4	c.-3-387delG		intron_variant	Intron 1 of 1	1	NM_130830.5	ENSP00000306276.4
LRRC15	ENST00000428839.1	c.16-387delG		intron_variant	Intron 2 of 2	1		ENSP00000413707.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82866 AN: 151990 Hom.: 24271 Cov.: 0

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.545 AC: 82943 AN: 152108 Hom.: 24304 Cov.: 0 AF XY: 0.539 AC XY: 40055 AN XY: 74332

African (AFR) AF: 0.770 AC: 31958 AN: 41506

American (AMR) AF: 0.415 AC: 6346 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1684 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3404 AN: 5164

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4816

European-Finnish (FIN) AF: 0.406 AC: 4294 AN: 10582

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31138 AN: 67970

Other (OTH) AF: 0.536 AC: 1129 AN: 2108

Alfa AF: 0.503 Hom.: 2518

Bravo AF: 0.557

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0
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: rs11313667; hg19: chr3-194082161;