rs1698041

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000717962.1(LSAMP):​n.536-141117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,096 control chromosomes in the GnomAD database, including 14,915 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 0.40 ( 14915 hom., cov: 32)

Consequence

LSAMP
ENST00000717962.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170

Publications

4 publications found
Variant links:
Genes affected
LSAMP (HGNC:6705): (limbic system associated membrane protein) This gene encodes a member of the immunoglobulin LAMP, OBCAM and neurotrimin (IgLON) family of proteins. The encoded preproprotein is proteolytically processed to generate a neuronal surface glycoprotein. This protein may act as a selective homophilic adhesion molecule during axon guidance and neuronal growth in the developing limbic system. The encoded protein may also function as a tumor suppressor and may play a role in neuropsychiatric disorders. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LSAMPENST00000717962.1 linkn.536-141117A>G intron_variant Intron 2 of 6

Frequencies

GnomAD3 genomes
AF:
0.405
AC:
61524
AN:
151978
Hom.:
14921
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.335
Gnomad ASJ
AF:
0.519
Gnomad EAS
AF:
0.231
Gnomad SAS
AF:
0.443
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.567
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.419
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.404
AC:
61500
AN:
152096
Hom.:
14915
Cov.:
32
AF XY:
0.399
AC XY:
29626
AN XY:
74324
show subpopulations
African (AFR)
AF:
0.152
AC:
6317
AN:
41532
American (AMR)
AF:
0.334
AC:
5105
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.519
AC:
1802
AN:
3470
East Asian (EAS)
AF:
0.230
AC:
1188
AN:
5158
South Asian (SAS)
AF:
0.443
AC:
2133
AN:
4820
European-Finnish (FIN)
AF:
0.495
AC:
5232
AN:
10560
Middle Eastern (MID)
AF:
0.566
AC:
164
AN:
290
European-Non Finnish (NFE)
AF:
0.564
AC:
38342
AN:
67970
Other (OTH)
AF:
0.414
AC:
877
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1627
3254
4880
6507
8134
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
574
1148
1722
2296
2870
<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:
0.455
Hom.:
5972
Bravo
AF:
0.378
Asia WGS
AF:
0.327
AC:
1141
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
14
DANN
Benign
0.70
PhyloP100
0.17
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs1698041; hg19: chr3-117199751; API