3-117707411-A-T

Variant names:

• chr3-117707411-A-T
• rs4132417
• ENST00000484092.1:n.412-35115T>A

Variant summary

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

The ENST00000484092.1(LINC03051):​n.412-35115T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,980 control chromosomes in the GnomAD database, including 4,902 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 0.25 (4902 hom., cov: 32)
• Consequence: LINC03051 ENST00000484092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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	ENST00000484092.1	n.412-35115T>A		intron_variant	Intron 1 of 1	4
LSAMP	ENST00000717962.1	n.535+21645T>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37247 AN: 151860 Hom.: 4895 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.245 AC: 37282 AN: 151980 Hom.: 4902 Cov.: 32 AF XY: 0.248 AC XY: 18390 AN XY: 74288

African (AFR) AF: 0.302 AC: 12501 AN: 41436

American (AMR) AF: 0.258 AC: 3929 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2040 AN: 5154

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10570

Middle Eastern (MID) AF: 0.324 AC: 94 AN: 290

European-Non Finnish (NFE) AF: 0.199 AC: 13528 AN: 67960

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.0948 Hom.: 119

Bravo AF: 0.252

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.65
PhyloP100		-0.089
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: rs4132417; hg19: chr3-117426258;