rs61988414

Positions:

• chr14-41844240-A-G

Variant summary

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

The NM_152447.5(LRFN5):​c.-20-42366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,058 control chromosomes in the GnomAD database, including 1,742 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 0.13 (1742 hom., cov: 31)
• Consequence: LRFN5 NM_152447.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

LRFN5 (HGNC:20360): (leucine rich repeat and fibronectin type III domain containing 5) This gene encodes a protein that belongs to the leucine-rich repeat and fibronectin type III domain-containing family of proteins. A similar protein in mouse, a glycosylated transmembrane protein, is thought to function in presynaptic differentiation. [provided by RefSeq, Sep 2016]

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 (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRFN5	NM_152447.5	c.-20-42366A>G		intron_variant		ENST00000298119.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRFN5	ENST00000298119.9	c.-20-42366A>G		intron_variant		1	NM_152447.5	P3
LRFN5	ENST00000554171.1	c.-20-42366A>G		intron_variant		1		A1
LRFN5	ENST00000554120.5	c.-20-42366A>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20324 AN: 151938 Hom.: 1743 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.0797

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.134 AC: 20326 AN: 152058 Hom.: 1742 Cov.: 31 AF XY: 0.130 AC XY: 9657 AN XY: 74322

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0987

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0798

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.132

Alfa AF: 0.158 Hom.: 238

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.15

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: rs61988414; hg19: chr14-42313443;