chr3-117459897-C-A

Variant names:

• chr3-117459897-C-A
• rs4356827
• ENST00000717962.1:n.536-120110G>T

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-120110G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,946 control chromosomes in the GnomAD database, including 23,795 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 0.56 (23795 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.944
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000717962.1		n.536-120110G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84333 AN: 151828 Hom.: 23801 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.555 AC: 84348 AN: 151946 Hom.: 23795 Cov.: 32 AF XY: 0.552 AC XY: 40994 AN XY: 74258

African (AFR) AF: 0.482 AC: 19950 AN: 41430

American (AMR) AF: 0.498 AC: 7598 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2009 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2322 AN: 5148

South Asian (SAS) AF: 0.706 AC: 3401 AN: 4816

European-Finnish (FIN) AF: 0.485 AC: 5128 AN: 10572

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42041 AN: 67946

Other (OTH) AF: 0.580 AC: 1222 AN: 2108

Alfa AF: 0.544 Hom.: 4016

Bravo AF: 0.546

Asia WGS AF: 0.559 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.57
PhyloP100		0.94
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: rs4356827; hg19: chr3-117178744;