rs1488454

Positions:

• chr3-3805121-C-T

Variant summary

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

The NM_020873.7(LRRN1):​c.-279+5202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,172 control chromosomes in the GnomAD database, including 53,711 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 0.84 (53711 hom., cov: 32)
• Consequence: LRRN1 NM_020873.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

LRRN1 (HGNC:20980): (leucine rich repeat neuronal 1) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

SUMF1 (HGNC:20376): (sulfatase modifying factor 1) This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRN1	NM_020873.7	c.-279+5202C>T		intron_variant		ENST00000319331.4
LRRN1	NM_001324188.2	c.-279+3875C>T		intron_variant
LRRN1	NM_001324189.2	c.-279+3875C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRN1	ENST00000319331.4	c.-279+5202C>T		intron_variant		1	NM_020873.7	P1
SUMF1	ENST00000448413.5	c.*343-16047G>A		intron_variant, NMD_transcript_variant		2
LRRN1	ENST00000496115.1	n.376+3875C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127669 AN: 152054 Hom.: 53676 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.840 AC: 127762 AN: 152172 Hom.: 53711 Cov.: 32 AF XY: 0.841 AC XY: 62570 AN XY: 74398

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.832

Alfa AF: 0.834 Hom.: 70600

Bravo AF: 0.838

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.36

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: rs1488454; hg19: chr3-3846805;