3-116465639-C-T

Variant names:

• chr3-116465639-C-T
• rs6787168
• ENST00000474851.1:c.179-20684G>A

Variant summary

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

The ENST00000474851.1(LSAMP):​c.179-20684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,866 control chromosomes in the GnomAD database, including 39,108 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 0.71 (39108 hom., cov: 31)
• Consequence: LSAMP ENST00000474851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 8 publications found

Genes affected

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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
LSAMP	ENST00000474851.1	c.179-20684G>A		intron_variant	Intron 2 of 4	5		ENSP00000418506.1
LSAMP	ENST00000717962.1	n.687-20684G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108294 AN: 151750 Hom.: 39115 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.713 AC: 108304 AN: 151866 Hom.: 39108 Cov.: 31 AF XY: 0.710 AC XY: 52731 AN XY: 74226

African (AFR) AF: 0.589 AC: 24392 AN: 41380

American (AMR) AF: 0.748 AC: 11422 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2642 AN: 3466

East Asian (EAS) AF: 0.827 AC: 4260 AN: 5154

South Asian (SAS) AF: 0.755 AC: 3639 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7195 AN: 10514

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52146 AN: 67946

Other (OTH) AF: 0.747 AC: 1576 AN: 2110

Alfa AF: 0.743 Hom.: 24249

Bravo AF: 0.712

Asia WGS AF: 0.755 AC: 2619 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.42
DANN	Benign	0.47
PhyloP100		0.068
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: rs6787168; hg19: chr3-116184486;