rs4831089

chr3-116253181-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LSAMP	NM_002338.5	c.156-166625C>T		intron_variant		ENST00000490035.7
LSAMP	NM_001318915.2	c.156-166625C>T		intron_variant
LSAMP	XM_011512840.4	c.156-166625C>T		intron_variant
LSAMP	XM_017006383.3	c.156-166625C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000490035.7	c.156-166625C>T		intron_variant		1	NM_002338.5	P1
LSAMP	ENST00000333617.8	c.108-166625C>T		intron_variant		2
LSAMP	ENST00000474851.1	c.258-166625C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.320

Alfa AF: 0.401 Hom.: 18671

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

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

Other links and lift over

dbSNP: rs4831089; hg19: chr3-115972028;