rs13088089

Variant names:

• chr3-117061175-A-C
• rs13088089
• ENST00000474851.1:c.34-51801T>G

Variant summary

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

The ENST00000717962.1(LSAMP):​n.594-51801T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,096 control chromosomes in the GnomAD database, including 5,206 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 0.24 (5206 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 6 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]

LOC124909415 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717962.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000474851.1	TSL:5	c.34-51801T>G		intron	N/A	ENSP00000418506.1	C9J5G3
	LSAMP	ENST00000717962.1		n.594-51801T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36519 AN: 151978 Hom.: 5209 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.240 AC: 36508 AN: 152096 Hom.: 5206 Cov.: 32 AF XY: 0.239 AC XY: 17749 AN XY: 74356

African (AFR) AF: 0.103 AC: 4284 AN: 41502

American (AMR) AF: 0.229 AC: 3499 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3470

East Asian (EAS) AF: 0.125 AC: 646 AN: 5168

South Asian (SAS) AF: 0.454 AC: 2190 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2269 AN: 10582

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21515 AN: 67960

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.303 Hom.: 8440

Bravo AF: 0.232

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13088089;

hg19: chr3-116780022;