chr14-41842228-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152447.5(LRFN5):​c.-20-44378T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,018 control chromosomes in the GnomAD database, including 2,599 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 0.18 ( 2599 hom., cov: 32)

Consequence

LRFN5
NM_152447.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0430

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRFN5NM_152447.5 linkc.-20-44378T>C intron_variant Intron 2 of 5 ENST00000298119.9 NP_689660.2 Q96NI6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LRFN5ENST00000298119.9 linkc.-20-44378T>C intron_variant Intron 2 of 5 1 NM_152447.5 ENSP00000298119.4 Q96NI6
LRFN5ENST00000554171.1 linkc.-20-44378T>C intron_variant Intron 4 of 6 1 ENSP00000451067.1 G3V364
LRFN5ENST00000554120.5 linkc.-20-44378T>C intron_variant Intron 2 of 3 5 ENSP00000451897.1 G3V4N1

Frequencies

GnomAD3 genomes
AF:
0.181
AC:
27558
AN:
151900
Hom.:
2593
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.194
Gnomad AMI
AF:
0.0932
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.0112
Gnomad SAS
AF:
0.140
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.194
Gnomad OTH
AF:
0.165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27604
AN:
152018
Hom.:
2599
Cov.:
32
AF XY:
0.176
AC XY:
13112
AN XY:
74298
show subpopulations
African (AFR)
AF:
0.194
AC:
8069
AN:
41510
American (AMR)
AF:
0.191
AC:
2911
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.114
AC:
397
AN:
3470
East Asian (EAS)
AF:
0.0112
AC:
58
AN:
5176
South Asian (SAS)
AF:
0.140
AC:
675
AN:
4824
European-Finnish (FIN)
AF:
0.177
AC:
1875
AN:
10588
Middle Eastern (MID)
AF:
0.0918
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
0.194
AC:
13164
AN:
67866
Other (OTH)
AF:
0.163
AC:
343
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1148
2296
3445
4593
5741
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
302
604
906
1208
1510
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.193
Hom.:
463
Bravo
AF:
0.187
Asia WGS
AF:
0.0800
AC:
276
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
4.4
DANN
Benign
0.42
PhyloP100
-0.043
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

Publications

Other links and lift over

dbSNP: rs12878452; hg19: chr14-42311431; API