3-116468864-T-C

Variant names:

• chr3-116468864-T-C
• rs16824996
• ENST00000474851.1:c.179-23909A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000717962.1(LSAMP):​n.687-23909A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,074 control chromosomes in the GnomAD database, including 3,058 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 0.19 (3058 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000474851.1	TSL:5	c.179-23909A>G		intron	N/A	ENSP00000418506.1	C9J5G3
	LSAMP	ENST00000717962.1		n.687-23909A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28287 AN: 151954 Hom.: 3059 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.186 AC: 28292 AN: 152074 Hom.: 3058 Cov.: 32 AF XY: 0.188 AC XY: 13983 AN XY: 74330

African (AFR) AF: 0.247 AC: 10233 AN: 41462

American (AMR) AF: 0.143 AC: 2182 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2348 AN: 5162

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4808

European-Finnish (FIN) AF: 0.152 AC: 1604 AN: 10574

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9394 AN: 67998

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.0678 Hom.: 78

Bravo AF: 0.190

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.49
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16824996;

hg19: chr3-116187711;