rs4687889

Variant names:

• chr3-117818592-T-C
• rs4687889
• ENST00000717944.1:c.68-89413A>G

Variant summary

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

The ENST00000717944.1(LINC03051):​c.68-89413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,950 control chromosomes in the GnomAD database, including 17,920 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 0.48 (17920 hom., cov: 32)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 8 publications found

Genes affected

LINC03051 (HGNC:56330): (long intergenic non-protein coding RNA 3051)

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
LINC03051	ENST00000717944.1	c.68-89413A>G		intron_variant	Intron 1 of 1			ENSP00000520652.1
LINC03051	ENST00000484092.1	n.412-146296A>G		intron_variant	Intron 1 of 1	4
LSAMP	ENST00000717962.1	n.412-89413A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72429 AN: 151832 Hom.: 17923 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.477 AC: 72453 AN: 151950 Hom.: 17920 Cov.: 32 AF XY: 0.470 AC XY: 34934 AN XY: 74254

African (AFR) AF: 0.560 AC: 23192 AN: 41428

American (AMR) AF: 0.502 AC: 7655 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3472

East Asian (EAS) AF: 0.0836 AC: 432 AN: 5166

South Asian (SAS) AF: 0.493 AC: 2373 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3855 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31824 AN: 67938

Other (OTH) AF: 0.485 AC: 1025 AN: 2112

Alfa AF: 0.477 Hom.: 32826

Bravo AF: 0.489

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.41
PhyloP100		0.29
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: rs4687889; hg19: chr3-117537439;