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 ENST00000474851.1(LSAMP):​c.34-51801T>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 ENST00000474851.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909415	XR_007096015.1	n.29330-51801T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000474851.1	c.34-51801T>G		intron_variant	Intron 1 of 4	5		ENSP00000418506.1
LSAMP	ENST00000717962.1	n.594-51801T>G		intron_variant	Intron 3 of 6

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 v4.3

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

Other links and lift over

dbSNP: rs13088089; hg19: chr3-116780022;