ENST00000717962.1:n.536-132358C>T

Variant names:

• chr3-117472145-G-A
• rs1910040
• ENST00000717962.1:n.536-132358C>T

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-132358C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 148,878 control chromosomes in the GnomAD database, including 32,680 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 0.65 (32680 hom., cov: 24)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000717962.1		n.536-132358C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 96662 AN: 148754 Hom.: 32675 Cov.: 24

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.650 AC: 96705 AN: 148878 Hom.: 32680 Cov.: 24 AF XY: 0.655 AC XY: 47434 AN XY: 72462

African (AFR) AF: 0.449 AC: 18114 AN: 40314

American (AMR) AF: 0.632 AC: 9311 AN: 14740

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2562 AN: 3448

East Asian (EAS) AF: 0.780 AC: 3956 AN: 5072

South Asian (SAS) AF: 0.753 AC: 3487 AN: 4632

European-Finnish (FIN) AF: 0.777 AC: 7902 AN: 10174

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49229 AN: 67264

Other (OTH) AF: 0.666 AC: 1356 AN: 2036

Alfa AF: 0.681 Hom.: 4471

Bravo AF: 0.625

Asia WGS AF: 0.735 AC: 2538 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-0.84
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: rs1910040; hg19: chr3-117190992;