rs1518898

chr3-117009701-C-Achr3-117009701-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007096015.1(LOC124909415):n.29330-327G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,076 control chromosomes in the GnomAD database, including 6,013 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 0.27 (6013 hom., cov: 32)
• Consequence: LOC124909415 XR_007096015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

Genes affected

LOC124909415 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909415	XR_007096015.1	n.29330-327G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000474851.1	c.34-327G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40347 AN: 151958 Hom.: 6011 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.265 AC: 40370 AN: 152076 Hom.: 6013 Cov.: 32 AF XY: 0.277 AC XY: 20628 AN XY: 74338

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.243

Alfa AF: 0.242 Hom.: 3219

Bravo AF: 0.255

Asia WGS AF: 0.458 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.72
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1518898; hg19: chr3-116728548;