3-115819804-G-C

Variant names:

• chr3-115819804-G-C
• rs9822311
• NM_002338.5:c.920-9390C>G

Variant summary

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

The NM_002338.5(LSAMP):​c.920-9390C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,088 control chromosomes in the GnomAD database, including 7,902 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 0.31 (7902 hom., cov: 31)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• 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]

ENSG00000297708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	NM_002338.5	MANE Select	c.920-9390C>G		intron	N/A	NP_002329.2
	LSAMP	NM_001318915.2		c.956-3158C>G		intron	N/A	NP_001305844.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000490035.7	TSL:1 MANE Select	c.920-9390C>G		intron	N/A	ENSP00000419000.1
	LSAMP	ENST00000333617.8	TSL:2	c.908-3158C>G		intron	N/A	ENSP00000328455.4
	LSAMP	ENST00000475403.2	TSL:3	n.226-3158C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47578 AN: 151970 Hom.: 7875 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.313 AC: 47646 AN: 152088 Hom.: 7902 Cov.: 31 AF XY: 0.305 AC XY: 22649 AN XY: 74356

African (AFR) AF: 0.415 AC: 17211 AN: 41472

American (AMR) AF: 0.317 AC: 4847 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3468

East Asian (EAS) AF: 0.115 AC: 596 AN: 5186

South Asian (SAS) AF: 0.170 AC: 819 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2351 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19919 AN: 67962

Other (OTH) AF: 0.310 AC: 654 AN: 2108

Alfa AF: 0.161 Hom.: 290

Bravo AF: 0.329

Asia WGS AF: 0.187 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.6
DANN	Benign	0.39
PhyloP100		-0.61
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: rs9822311; hg19: chr3-115538651;