3-117152001-T-C

Variant names:

• chr3-117152001-T-C
• rs6788787
• ENST00000717962.1:n.594-142627A>G

Variant summary

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

The ENST00000717962.1(LSAMP):​n.594-142627A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,166 control chromosomes in the GnomAD database, including 59,586 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 0.88 (59586 hom., cov: 31)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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	ENST00000717962.1		n.594-142627A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134417 AN: 152048 Hom.: 59523 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.884 AC: 134540 AN: 152166 Hom.: 59586 Cov.: 31 AF XY: 0.888 AC XY: 66032 AN XY: 74386

African (AFR) AF: 0.915 AC: 37996 AN: 41524

American (AMR) AF: 0.908 AC: 13883 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3053 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5116 AN: 5154

South Asian (SAS) AF: 0.863 AC: 4149 AN: 4808

European-Finnish (FIN) AF: 0.907 AC: 9604 AN: 10590

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57842 AN: 68014

Other (OTH) AF: 0.883 AC: 1867 AN: 2114

Alfa AF: 0.869 Hom.: 50270

Bravo AF: 0.887

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.41
PhyloP100		-0.64
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: rs6788787; hg19: chr3-116870848;