chr3-117887069-A-G

Variant names:

• chr3-117887069-A-G
• rs4277680
• ENST00000717944.1:c.67+110113T>C

Variant summary

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

The ENST00000717944.1(LINC03051):​c.67+110113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,774 control chromosomes in the GnomAD database, including 11,544 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 0.39 (11544 hom., cov: 32)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717944.1. 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
	LINC03051	NR_182298.1		n.399-8263T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03051	ENST00000717944.1		c.67+110113T>C		intron	N/A	ENSP00000520652.1	A0ABB0MV48
	LINC03051	ENST00000484092.1	TSL:4	n.411+110113T>C		intron	N/A
	LINC03051	ENST00000665851.1		n.399-8263T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58890 AN: 151656 Hom.: 11536 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 58938 AN: 151774 Hom.: 11544 Cov.: 32 AF XY: 0.390 AC XY: 28902 AN XY: 74172

African (AFR) AF: 0.364 AC: 15084 AN: 41446

American (AMR) AF: 0.405 AC: 6156 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1530 AN: 3464

East Asian (EAS) AF: 0.582 AC: 2976 AN: 5114

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4822

European-Finnish (FIN) AF: 0.392 AC: 4140 AN: 10574

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26111 AN: 67838

Other (OTH) AF: 0.388 AC: 816 AN: 2104

Alfa AF: 0.382 Hom.: 2205

Bravo AF: 0.390

Asia WGS AF: 0.437 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.58
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4277680;

hg19: chr3-117605916;