NM_002338.5:c.155+2190A>T

Variant names:

• chr3-116442687-T-A
• rs9822445
• NM_002338.5:c.155+2190A>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.155+2190A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,030 control chromosomes in the GnomAD database, including 24,615 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 0.53 (24615 hom., cov: 32)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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+2190A>T		intron	N/A	NP_002329.2
	LSAMP	NM_001318915.2		c.155+2190A>T		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+2190A>T		intron	N/A	ENSP00000419000.1
	LSAMP	ENST00000333617.8	TSL:2	c.107+2190A>T		intron	N/A	ENSP00000328455.4
	LSAMP	ENST00000474851.1	TSL:5	c.257+2190A>T		intron	N/A	ENSP00000418506.1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81230 AN: 151910 Hom.: 24624 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.534 AC: 81218 AN: 152030 Hom.: 24615 Cov.: 32 AF XY: 0.538 AC XY: 39957 AN XY: 74306

African (AFR) AF: 0.222 AC: 9198 AN: 41480

American (AMR) AF: 0.600 AC: 9174 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3709 AN: 5146

South Asian (SAS) AF: 0.711 AC: 3424 AN: 4816

European-Finnish (FIN) AF: 0.616 AC: 6502 AN: 10554

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45106 AN: 67964

Other (OTH) AF: 0.574 AC: 1210 AN: 2108

Alfa AF: 0.447 Hom.: 1405

Bravo AF: 0.519

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.68
PhyloP100		0.90
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: rs9822445; hg19: chr3-116161534;