NM_002338.5:c.155+64683G>A

Variant names:

• chr3-116380194-C-T
• rs17647013
• NM_002338.5:c.155+64683G>A

Variant summary

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

The NM_002338.5(LSAMP):​c.155+64683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 151,830 control chromosomes in the GnomAD database, including 402 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 0.062 (402 hom., cov: 32)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• 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]

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 (NFE) allele frequency at 95% confidence interval = 0.0901 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.155+64683G>A		intron	N/A	NP_002329.2
	LSAMP	NM_001318915.2		c.155+64683G>A		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.155+64683G>A		intron	N/A	ENSP00000419000.1
	LSAMP	ENST00000333617.8	TSL:2	c.107+64683G>A		intron	N/A	ENSP00000328455.4
	LSAMP	ENST00000474851.1	TSL:5	c.257+64683G>A		intron	N/A	ENSP00000418506.1

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9488 AN: 151712 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0571

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

GnomAD4 genome AF: 0.0625 AC: 9486 AN: 151830 Hom.: 402 Cov.: 32 AF XY: 0.0623 AC XY: 4628 AN XY: 74232

African (AFR) AF: 0.0157 AC: 648 AN: 41362

American (AMR) AF: 0.0529 AC: 805 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3468

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.0705 AC: 339 AN: 4806

European-Finnish (FIN) AF: 0.0901 AC: 952 AN: 10564

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6247 AN: 67930

Other (OTH) AF: 0.0560 AC: 118 AN: 2106

Alfa AF: 0.0690 Hom.: 371

Bravo AF: 0.0575

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.55
PhyloP100		-0.035
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: rs17647013; hg19: chr3-116099041;