3-117224163-T-C

Variant names:

• chr3-117224163-T-C
• rs1462845
• ENST00000717962.1:n.593+115567A>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+115567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,084 control chromosomes in the GnomAD database, including 14,763 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 0.43 (14763 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 6 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]

LOC124909415 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909415	XR_007096015.1	n.29329+24853A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000717962.1	n.593+115567A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65075 AN: 151966 Hom.: 14736 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.428 AC: 65147 AN: 152084 Hom.: 14763 Cov.: 32 AF XY: 0.428 AC XY: 31793 AN XY: 74362

African (AFR) AF: 0.539 AC: 22360 AN: 41450

American (AMR) AF: 0.473 AC: 7228 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3667 AN: 5162

South Asian (SAS) AF: 0.432 AC: 2085 AN: 4828

European-Finnish (FIN) AF: 0.286 AC: 3024 AN: 10584

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23704 AN: 67996

Other (OTH) AF: 0.450 AC: 952 AN: 2114

Alfa AF: 0.381 Hom.: 35698

Bravo AF: 0.449

Asia WGS AF: 0.552 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		1.6
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: rs1462845; hg19: chr3-116943010;