rs6438424

Variant names:

• chr3-117855975-A-C
• rs6438424
• ENST00000717944.1:c.68-126796T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-117855975-A-C
• chr3-117855975-A-T

Variant summary

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

The ENST00000717944.1(LINC03051):​c.68-126796T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,932 control chromosomes in the GnomAD database, including 15,545 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 0.44 (15545 hom., cov: 32)
• Consequence: LINC03051 ENST00000717944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 30 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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.68-126796T>G		intron_variant	Intron 1 of 1			ENSP00000520652.1
LINC03051	ENST00000484092.1	n.411+141207T>G		intron_variant	Intron 1 of 1	4
LSAMP	ENST00000717962.1	n.412-126796T>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66282 AN: 151812 Hom.: 15545 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 66306 AN: 151932 Hom.: 15545 Cov.: 32 AF XY: 0.442 AC XY: 32860 AN XY: 74284

African (AFR) AF: 0.264 AC: 10938 AN: 41424

American (AMR) AF: 0.431 AC: 6587 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3117 AN: 5154

South Asian (SAS) AF: 0.416 AC: 2007 AN: 4828

European-Finnish (FIN) AF: 0.602 AC: 6360 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34083 AN: 67910

Other (OTH) AF: 0.430 AC: 907 AN: 2108

Alfa AF: 0.477 Hom.: 48631

Bravo AF: 0.418

Asia WGS AF: 0.484 AC: 1675 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		0.094
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: rs6438424; hg19: chr3-117574822;