rs6076920

chr20-6048671-C-G

Variant summary

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

The NM_152611.5(LRRN4):c.860+2108G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 152,224 control chromosomes in the GnomAD database, including 891 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 0.099 (891 hom., cov: 32)
• Consequence: LRRN4 NM_152611.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

LRRN4 (HGNC:16208): (leucine rich repeat neuronal 4) Predicted to be involved in long-term memory. Predicted to act upstream of or within visual learning. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRN4	NM_152611.5	c.860+2108G>C		intron_variant		ENST00000378858.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRN4	ENST00000378858.5	c.860+2108G>C		intron_variant		1	NM_152611.5	P1
LRRN4	ENST00000698795.1	c.860+2108G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 15014 AN: 152106 Hom.: 889 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0987 AC: 15026 AN: 152224 Hom.: 891 Cov.: 32 AF XY: 0.0996 AC XY: 7414 AN XY: 74420

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0913

Gnomad4 SAS AF: 0.0647

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.121

Alfa AF: 0.101 Hom.: 101

Bravo AF: 0.0948

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs6076920; hg19: chr20-6029317;