rs1106851

Variant names:

• chr3-116742462-G-A
• rs1106851
• ENST00000474851.1:c.178+266768C>T

Variant summary

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

The ENST00000474851.1(LSAMP):​c.178+266768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,360 control chromosomes in the GnomAD database, including 2,761 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 0.19 (2761 hom., cov: 30)
• Consequence: LSAMP ENST00000474851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000474851.1	c.178+266768C>T		intron_variant	Intron 2 of 4	5		ENSP00000418506.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28688 AN: 151276 Hom.: 2763 Cov.: 30

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.190 AC: 28690 AN: 151360 Hom.: 2761 Cov.: 30 AF XY: 0.189 AC XY: 13981 AN XY: 73894

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.177

Alfa AF: 0.202 Hom.: 401

Bravo AF: 0.185

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.76
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1106851; hg19: chr3-116461309;