rs1698041

Variant names:

• chr3-117480904-T-C
• rs1698041
• ENST00000717962.1:n.536-141117A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000717962.1(LSAMP):​n.536-141117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,096 control chromosomes in the GnomAD database, including 14,915 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 0.40 (14915 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000717962.1		n.536-141117A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61524 AN: 151978 Hom.: 14921 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.404 AC: 61500 AN: 152096 Hom.: 14915 Cov.: 32 AF XY: 0.399 AC XY: 29626 AN XY: 74324

African (AFR) AF: 0.152 AC: 6317 AN: 41532

American (AMR) AF: 0.334 AC: 5105 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1188 AN: 5158

South Asian (SAS) AF: 0.443 AC: 2133 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5232 AN: 10560

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.564 AC: 38342 AN: 67970

Other (OTH) AF: 0.414 AC: 877 AN: 2116

Alfa AF: 0.455 Hom.: 5972

Bravo AF: 0.378

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.17
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: rs1698041; hg19: chr3-117199751;