chr3-116861250-C-T

Variant names:

• chr3-116861250-C-T
• rs13092348
• ENST00000474851.1:c.178+147980G>A

Variant summary

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

The ENST00000474851.1(LSAMP):​c.178+147980G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,014 control chromosomes in the GnomAD database, including 4,611 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 0.24 (4611 hom., cov: 32)
• Consequence: LSAMP ENST00000474851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000474851.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000474851.1	TSL:5	c.178+147980G>A		intron	N/A	ENSP00000418506.1
	LSAMP	ENST00000717962.1		n.686+148032G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35741 AN: 151896 Hom.: 4605 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.235 AC: 35782 AN: 152014 Hom.: 4611 Cov.: 32 AF XY: 0.236 AC XY: 17500 AN XY: 74290

African (AFR) AF: 0.146 AC: 6051 AN: 41476

American (AMR) AF: 0.215 AC: 3286 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5166

South Asian (SAS) AF: 0.447 AC: 2153 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2362 AN: 10566

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19117 AN: 67940

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.238 Hom.: 616

Bravo AF: 0.226

Asia WGS AF: 0.260 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.37
PhyloP100		-3.5
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: rs13092348; hg19: chr3-116580097;