rs4831089

Variant names:

• chr3-116253181-G-A
• rs4831089
• NM_002338.5:c.156-166625C>T

Variant summary

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

The NM_002338.5(LSAMP):​c.156-166625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,700 control chromosomes in the GnomAD database, including 9,563 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 0.32 (9563 hom., cov: 32)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.156-166625C>T		intron_variant	Intron 1 of 6	ENST00000490035.7	NP_002329.2
LSAMP	NM_001318915.2	c.156-166625C>T		intron_variant	Intron 1 of 8		NP_001305844.1
LSAMP	XM_017006383.3	c.156-166625C>T		intron_variant	Intron 1 of 7		XP_016861872.1
LSAMP	XM_011512840.4	c.156-166625C>T		intron_variant	Intron 1 of 7		XP_011511142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000490035.7	c.156-166625C>T		intron_variant	Intron 1 of 6	1	NM_002338.5	ENSP00000419000.1
LSAMP	ENST00000333617.8	c.108-166625C>T		intron_variant	Intron 1 of 8	2		ENSP00000328455.4
LSAMP	ENST00000474851.1	c.258-166625C>T		intron_variant	Intron 3 of 4	5		ENSP00000418506.1
LSAMP	ENST00000717962.1	n.766-166625C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48279 AN: 151580 Hom.: 9567 Cov.: 32

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.318 AC: 48266 AN: 151700 Hom.: 9563 Cov.: 32 AF XY: 0.320 AC XY: 23685 AN XY: 74106

African (AFR) AF: 0.0798 AC: 3299 AN: 41328

American (AMR) AF: 0.330 AC: 5032 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2471 AN: 5142

South Asian (SAS) AF: 0.337 AC: 1616 AN: 4796

European-Finnish (FIN) AF: 0.427 AC: 4483 AN: 10502

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28872 AN: 67906

Other (OTH) AF: 0.320 AC: 674 AN: 2106

Alfa AF: 0.374 Hom.: 27856

Bravo AF: 0.301

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.57
PhyloP100		-0.43
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

Other links and lift over

dbSNP: rs4831089; hg19: chr3-115972028;