rs2918213

Variant names:

• chr3-115833592-G-A
• rs2918213
• NM_002338.5:c.919+8253C>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.919+8253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,982 control chromosomes in the GnomAD database, including 15,665 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 0.44 (15665 hom., cov: 33)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 5 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]

ENSG00000297708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002338.5. 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
	LSAMP	NM_002338.5	MANE Select	c.919+8253C>T		intron	N/A	NP_002329.2
	LSAMP	NM_001318915.2		c.955+970C>T		intron	N/A	NP_001305844.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000490035.7	TSL:1 MANE Select	c.919+8253C>T		intron	N/A	ENSP00000419000.1	Q13449
	LSAMP	ENST00000333617.8	TSL:2	c.907+970C>T		intron	N/A	ENSP00000328455.4	H3BLU2
	LSAMP	ENST00000475403.2	TSL:3	n.225+970C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67514 AN: 151864 Hom.: 15649 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.445 AC: 67564 AN: 151982 Hom.: 15665 Cov.: 33 AF XY: 0.442 AC XY: 32822 AN XY: 74298

African (AFR) AF: 0.580 AC: 24065 AN: 41462

American (AMR) AF: 0.509 AC: 7778 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1590 AN: 5176

South Asian (SAS) AF: 0.321 AC: 1549 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3681 AN: 10556

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26161 AN: 67908

Other (OTH) AF: 0.451 AC: 954 AN: 2114

Alfa AF: 0.433 Hom.: 2373

Bravo AF: 0.463

Asia WGS AF: 0.340 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.45
PhyloP100		-0.037
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: rs2918213; hg19: chr3-115552439;