rs1884641

Variant names:

• chr20-6059263-A-C
• rs1884641
• ENST00000903106.1:c.-6+934T>G

Variant summary

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

The ENST00000903106.1(LRRN4):​c.-6+934T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,252 control chromosomes in the GnomAD database, including 4,133 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 (4133 hom., cov: 33)
• Consequence: LRRN4 ENST00000903106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 8 publications found

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]

LOC124904865 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000903106.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRN4	ENST00000903106.1		c.-6+934T>G		intron	N/A	ENSP00000573165.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31241 AN: 152134 Hom.: 4127 Cov.: 33

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.205 AC: 31261 AN: 152252 Hom.: 4133 Cov.: 33 AF XY: 0.205 AC XY: 15274 AN XY: 74438

African (AFR) AF: 0.0668 AC: 2778 AN: 41566

American (AMR) AF: 0.350 AC: 5344 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2134 AN: 5166

South Asian (SAS) AF: 0.249 AC: 1201 AN: 4830

European-Finnish (FIN) AF: 0.161 AC: 1709 AN: 10602

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16738 AN: 68006

Other (OTH) AF: 0.221 AC: 468 AN: 2116

Alfa AF: 0.237 Hom.: 15745

Bravo AF: 0.214

Asia WGS AF: 0.360 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1884641;

hg19: chr20-6039909;