ENST00000717944.1:c.67+123681G>T

Variant names:

• chr3-117873501-C-A
• rs6804394
• ENST00000717944.1:c.67+123681G>T

Variant summary

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

The ENST00000717944.1(LINC03051):​c.67+123681G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,926 control chromosomes in the GnomAD database, including 18,226 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 0.49 (18226 hom., cov: 31)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 2 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 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.67+123681G>T		intron_variant	Intron 1 of 1			ENSP00000520652.1
LINC03051	ENST00000484092.1	n.411+123681G>T		intron_variant	Intron 1 of 1	4
LSAMP	ENST00000717962.1	n.411+123681G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73848 AN: 151808 Hom.: 18202 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.487 AC: 73924 AN: 151926 Hom.: 18226 Cov.: 31 AF XY: 0.490 AC XY: 36383 AN XY: 74258

African (AFR) AF: 0.431 AC: 17844 AN: 41404

American (AMR) AF: 0.455 AC: 6937 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3466

East Asian (EAS) AF: 0.596 AC: 3076 AN: 5160

South Asian (SAS) AF: 0.418 AC: 2009 AN: 4806

European-Finnish (FIN) AF: 0.604 AC: 6365 AN: 10546

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34289 AN: 67974

Other (OTH) AF: 0.472 AC: 996 AN: 2112

Alfa AF: 0.475 Hom.: 7554

Bravo AF: 0.475

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		0.27
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: rs6804394; hg19: chr3-117592348;