rs1106851

Variant names:

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

Variant summary

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

The ENST00000717962.1(LSAMP):​n.686+266820C>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 ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.178+266768C>T		intron	N/A	ENSP00000418506.1	C9J5G3
	LSAMP	ENST00000717962.1		n.686+266820C>T		intron	N/A

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

African (AFR) AF: 0.177 AC: 7308 AN: 41254

American (AMR) AF: 0.156 AC: 2377 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3462

East Asian (EAS) AF: 0.180 AC: 928 AN: 5142

South Asian (SAS) AF: 0.180 AC: 862 AN: 4784

European-Finnish (FIN) AF: 0.185 AC: 1908 AN: 10304

Middle Eastern (MID) AF: 0.260 AC: 75 AN: 288

European-Non Finnish (NFE) AF: 0.201 AC: 13676 AN: 67914

Other (OTH) AF: 0.177 AC: 372 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.76
DANN	Benign	0.52
PhyloP100		-0.52
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: rs1106851; hg19: chr3-116461309;