rs1676232

Variant names:

• chr3-117515992-G-A
• rs1676232
• ENST00000717962.1:n.536-176205C>T

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-176205C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,936 control chromosomes in the GnomAD database, including 19,742 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 (19742 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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.536-176205C>T		intron	N/A
	ENSG00000303790	ENST00000797238.1		n.156+1492G>A		intron	N/A
	ENSG00000303790	ENST00000797242.1		n.259-239G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71998 AN: 151818 Hom.: 19745 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.474 AC: 71983 AN: 151936 Hom.: 19742 Cov.: 32 AF XY: 0.471 AC XY: 34919 AN XY: 74214

African (AFR) AF: 0.207 AC: 8562 AN: 41460

American (AMR) AF: 0.418 AC: 6370 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5160

South Asian (SAS) AF: 0.499 AC: 2398 AN: 4806

European-Finnish (FIN) AF: 0.604 AC: 6355 AN: 10522

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42871 AN: 67960

Other (OTH) AF: 0.499 AC: 1050 AN: 2106

Alfa AF: 0.580 Hom.: 112138

Bravo AF: 0.444

Asia WGS AF: 0.393 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.3
DANN	Benign	0.57
PhyloP100		1.1
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: rs1676232; hg19: chr3-117234839;