rs13088089

Positions:

• chr3-117061175-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124909415	XR_007096015.1	n.29330-51801T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000474851.1	c.34-51801T>G		intron_variant		5		ENSP00000418506.1

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.262

Alfa AF: 0.305 Hom.: 7190

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13088089; hg19: chr3-116780022;