3-116366831-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002338.5(LSAMP):​c.155+78046T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,002 control chromosomes in the GnomAD database, including 54,140 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 ( 54140 hom., cov: 30)

Consequence

LSAMP
NM_002338.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.17
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LSAMPNM_002338.5 linkuse as main transcriptc.155+78046T>A intron_variant ENST00000490035.7 NP_002329.2 Q13449B7Z661

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LSAMPENST00000490035.7 linkuse as main transcriptc.155+78046T>A intron_variant 1 NM_002338.5 ENSP00000419000.1 Q13449
LSAMPENST00000333617.8 linkuse as main transcriptc.107+78046T>A intron_variant 2 ENSP00000328455.4 H3BLU2
LSAMPENST00000474851.1 linkuse as main transcriptc.257+78046T>A intron_variant 5 ENSP00000418506.1 C9J5G3
LSAMP-AS1ENST00000490351.1 linkuse as main transcriptn.71-1111A>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.842
AC:
127850
AN:
151886
Hom.:
54096
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.886
Gnomad AMI
AF:
0.871
Gnomad AMR
AF:
0.803
Gnomad ASJ
AF:
0.842
Gnomad EAS
AF:
0.945
Gnomad SAS
AF:
0.927
Gnomad FIN
AF:
0.708
Gnomad MID
AF:
0.915
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.861
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.842
AC:
127942
AN:
152002
Hom.:
54140
Cov.:
30
AF XY:
0.837
AC XY:
62215
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.886
Gnomad4 AMR
AF:
0.802
Gnomad4 ASJ
AF:
0.842
Gnomad4 EAS
AF:
0.945
Gnomad4 SAS
AF:
0.927
Gnomad4 FIN
AF:
0.708
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.860
Alfa
AF:
0.756
Hom.:
2187
Bravo
AF:
0.849
Asia WGS
AF:
0.906
AC:
3152
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.042
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs988803; hg19: chr3-116085678; API