chr3-117746384-G-A

Variant names:

• chr3-117746384-G-A
• rs4687991
• ENST00000717944.1:c.68-17205C>T

Variant summary

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

The ENST00000717944.1(LINC03051):​c.68-17205C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,904 control chromosomes in the GnomAD database, including 23,505 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 0.54 (23505 hom., cov: 32)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 3 publications found

Genes affected

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

ENSG00000242816 (HGNC:):

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101926953	NR_188507.1	n.443+3273G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03051	ENST00000717944.1	c.68-17205C>T		intron_variant	Intron 1 of 1			ENSP00000520652.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81773 AN: 151786 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.539 AC: 81801 AN: 151904 Hom.: 23505 Cov.: 32 AF XY: 0.538 AC XY: 39887 AN XY: 74204

African (AFR) AF: 0.341 AC: 14145 AN: 41454

American (AMR) AF: 0.703 AC: 10738 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1843 AN: 5102

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4816

European-Finnish (FIN) AF: 0.533 AC: 5629 AN: 10552

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42458 AN: 67914

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.607 Hom.: 16595

Bravo AF: 0.540

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.42
PhyloP100		-0.23
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: rs4687991; hg19: chr3-117465231;