3-117519913-A-T

Variant names:

• chr3-117519913-A-T
• rs1393189
• ENST00000717962.1:n.536-180126T>A

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-180126T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,092 control chromosomes in the GnomAD database, including 11,062 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 0.36 (11062 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• 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]

ENSG00000303790 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374056	XR_924361.3	n.30063+5413A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000717962.1	n.536-180126T>A		intron_variant	Intron 2 of 6
ENSG00000303790	ENST00000797238.1	n.156+5413A>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55117 AN: 151974 Hom.: 11042 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.363 AC: 55177 AN: 152092 Hom.: 11062 Cov.: 32 AF XY: 0.373 AC XY: 27714 AN XY: 74350

African (AFR) AF: 0.208 AC: 8648 AN: 41506

American (AMR) AF: 0.482 AC: 7360 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3609 AN: 5150

South Asian (SAS) AF: 0.507 AC: 2446 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4755 AN: 10586

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.380 AC: 25817 AN: 67956

Other (OTH) AF: 0.366 AC: 774 AN: 2116

Alfa AF: 0.254 Hom.: 674

Bravo AF: 0.356

Asia WGS AF: 0.562 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.78
DANN	Benign	0.49
PhyloP100		0.079
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: rs1393189; hg19: chr3-117238760;