3-117293041-T-C

Variant names:

• chr3-117293041-T-C
• rs1513172
• ENST00000717962.1:n.593+46689A>G

Variant summary

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

The ENST00000717962.1(LSAMP):​n.593+46689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,538 control chromosomes in the GnomAD database, including 18,565 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 0.47 (18565 hom., cov: 31)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000717962.1	n.593+46689A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70709 AN: 151420 Hom.: 18550 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.467 AC: 70777 AN: 151538 Hom.: 18565 Cov.: 31 AF XY: 0.474 AC XY: 35084 AN XY: 74024

African (AFR) AF: 0.695 AC: 28786 AN: 41392

American (AMR) AF: 0.398 AC: 6040 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 959 AN: 3454

East Asian (EAS) AF: 0.668 AC: 3400 AN: 5088

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5305 AN: 10546

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22536 AN: 67758

Other (OTH) AF: 0.426 AC: 894 AN: 2098

Alfa AF: 0.377 Hom.: 24012

Bravo AF: 0.470

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.76
PhyloP100		0.14
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: rs1513172; hg19: chr3-117011888;