3-117826130-T-C

Variant names:

• chr3-117826130-T-C
• rs6438414
• ENST00000717944.1:c.68-96951A>G

Variant summary

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

The ENST00000717944.1(LINC03051):​c.68-96951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,766 control chromosomes in the GnomAD database, including 23,838 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 (23838 hom., cov: 31)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.673 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.68-96951A>G		intron_variant	Intron 1 of 1			ENSP00000520652.1
LINC03051	ENST00000484092.1	n.412-153834A>G		intron_variant	Intron 1 of 1	4
LSAMP	ENST00000717962.1	n.412-96951A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84365 AN: 151648 Hom.: 23827 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.556 AC: 84426 AN: 151766 Hom.: 23838 Cov.: 31 AF XY: 0.558 AC XY: 41338 AN XY: 74146

African (AFR) AF: 0.486 AC: 20104 AN: 41358

American (AMR) AF: 0.684 AC: 10397 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2241 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3259 AN: 5130

South Asian (SAS) AF: 0.485 AC: 2337 AN: 4820

European-Finnish (FIN) AF: 0.551 AC: 5809 AN: 10548

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38315 AN: 67922

Other (OTH) AF: 0.580 AC: 1223 AN: 2110

Alfa AF: 0.576 Hom.: 43220

Bravo AF: 0.564

Asia WGS AF: 0.546 AC: 1896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.85
PhyloP100		0.48
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: rs6438414; hg19: chr3-117544977;