rs1354152

Variant names:

• chr3-117474331-T-C
• rs1354152
• ENST00000717962.1:n.536-134544A>G

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-134544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,914 control chromosomes in the GnomAD database, including 14,798 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 (14798 hom., cov: 31)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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
LSAMP	ENST00000717962.1	n.536-134544A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61252 AN: 151796 Hom.: 14804 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.403 AC: 61226 AN: 151914 Hom.: 14798 Cov.: 31 AF XY: 0.397 AC XY: 29496 AN XY: 74232

African (AFR) AF: 0.152 AC: 6305 AN: 41480

American (AMR) AF: 0.333 AC: 5078 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1178 AN: 5150

South Asian (SAS) AF: 0.445 AC: 2139 AN: 4810

European-Finnish (FIN) AF: 0.496 AC: 5216 AN: 10526

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38145 AN: 67918

Other (OTH) AF: 0.413 AC: 871 AN: 2108

Alfa AF: 0.447 Hom.: 3017

Bravo AF: 0.376

Asia WGS AF: 0.327 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1354152; hg19: chr3-117193178;