rs1381801

Variant names:

• chr3-117522048-A-T
• rs1381801
• ENST00000717962.1:n.536-182261T>A

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-182261T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,010 control chromosomes in the GnomAD database, including 19,434 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 0.49 (19434 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 4 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]

ENSG00000303790 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717962.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000717962.1		n.536-182261T>A		intron	N/A
	ENSG00000303790	ENST00000797238.1		n.156+7548A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74054 AN: 151892 Hom.: 19435 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.487 AC: 74061 AN: 152010 Hom.: 19434 Cov.: 32 AF XY: 0.481 AC XY: 35737 AN XY: 74306

African (AFR) AF: 0.321 AC: 13310 AN: 41444

American (AMR) AF: 0.456 AC: 6967 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1884 AN: 3464

East Asian (EAS) AF: 0.202 AC: 1044 AN: 5168

South Asian (SAS) AF: 0.444 AC: 2142 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5714 AN: 10558

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41095 AN: 67966

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.534 Hom.: 2792

Bravo AF: 0.476

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.37
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: rs1381801; hg19: chr3-117240895;