14-41718713-A-G

Variant names:

• chr14-41718713-A-G
• rs10149831
• NM_152447.5:c.-196-48141A>G

Variant summary

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

The NM_152447.5(LRFN5):​c.-196-48141A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,988 control chromosomes in the GnomAD database, including 27,301 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 0.59 (27301 hom., cov: 32)
• Consequence: LRFN5 NM_152447.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152447.5. 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
	LRFN5	NM_152447.5	MANE Select	c.-196-48141A>G		intron	N/A	NP_689660.2
	LRFN5	NM_001346173.2		c.-21+110151A>G		intron	N/A	NP_001333102.1	Q96NI6
	LRFN5	NM_001330106.2		c.-196-48141A>G		intron	N/A	NP_001317035.1	G3V364

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRFN5	ENST00000298119.9	TSL:1 MANE Select	c.-196-48141A>G		intron	N/A	ENSP00000298119.4	Q96NI6
	LRFN5	ENST00000554171.1	TSL:1	c.-312-12624A>G		intron	N/A	ENSP00000451067.1	G3V364
	LRFN5	ENST00000935948.1		c.-173-48164A>G		intron	N/A	ENSP00000606007.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89891 AN: 151870 Hom.: 27270 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.592 AC: 89976 AN: 151988 Hom.: 27301 Cov.: 32 AF XY: 0.583 AC XY: 43285 AN XY: 74290

African (AFR) AF: 0.736 AC: 30523 AN: 41482

American (AMR) AF: 0.553 AC: 8445 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1943 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2656 AN: 5142

South Asian (SAS) AF: 0.555 AC: 2671 AN: 4812

European-Finnish (FIN) AF: 0.432 AC: 4565 AN: 10566

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37245 AN: 67944

Other (OTH) AF: 0.586 AC: 1237 AN: 2110

Alfa AF: 0.564 Hom.: 76062

Bravo AF: 0.610

Asia WGS AF: 0.549 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.30
PhyloP100		-1.1
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: rs10149831; hg19: chr14-42187916;