3-117472934-T-C

Variant names:

• chr3-117472934-T-C
• rs1501885
• ENST00000717962.1:n.536-133147A>G

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-133147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,880 control chromosomes in the GnomAD database, including 14,707 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 (14707 hom., cov: 31)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• 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 = 0.557 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.536-133147A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60665 AN: 151762 Hom.: 14713 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.399 AC: 60633 AN: 151880 Hom.: 14707 Cov.: 31 AF XY: 0.394 AC XY: 29209 AN XY: 74216

African (AFR) AF: 0.138 AC: 5737 AN: 41508

American (AMR) AF: 0.331 AC: 5041 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1792 AN: 3460

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5154

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4812

European-Finnish (FIN) AF: 0.496 AC: 5221 AN: 10530

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38152 AN: 67886

Other (OTH) AF: 0.410 AC: 864 AN: 2108

Alfa AF: 0.458 Hom.: 2364

Bravo AF: 0.372

Asia WGS AF: 0.325 AC: 1132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		-0.30
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: rs1501885; hg19: chr3-117191781;