chr3-116305143-C-T

Variant names:

• chr3-116305143-C-T
• rs2100807
• NM_002338.5:c.155+139734G>A

Variant summary

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

The NM_002338.5(LSAMP):​c.155+139734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,990 control chromosomes in the GnomAD database, including 41,746 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 0.72 (41746 hom., cov: 31)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 6 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]

LSAMP-AS1 (HGNC:40350): (LSAMP antisense RNA 1)

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 = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.155+139734G>A		intron_variant	Intron 1 of 6	ENST00000490035.7	NP_002329.2
LSAMP	NM_001318915.2	c.155+139734G>A		intron_variant	Intron 1 of 8		NP_001305844.1
LSAMP	XM_017006383.3	c.155+139734G>A		intron_variant	Intron 1 of 7		XP_016861872.1
LSAMP	XM_011512840.4	c.155+139734G>A		intron_variant	Intron 1 of 7		XP_011511142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000490035.7	c.155+139734G>A		intron_variant	Intron 1 of 6	1	NM_002338.5	ENSP00000419000.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109244 AN: 151872 Hom.: 41734 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.719 AC: 109290 AN: 151990 Hom.: 41746 Cov.: 31 AF XY: 0.727 AC XY: 54024 AN XY: 74318

African (AFR) AF: 0.438 AC: 18142 AN: 41436

American (AMR) AF: 0.809 AC: 12334 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2609 AN: 3468

East Asian (EAS) AF: 0.910 AC: 4685 AN: 5146

South Asian (SAS) AF: 0.822 AC: 3968 AN: 4828

European-Finnish (FIN) AF: 0.886 AC: 9398 AN: 10604

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55709 AN: 67944

Other (OTH) AF: 0.712 AC: 1497 AN: 2104

Alfa AF: 0.765 Hom.: 88156

Bravo AF: 0.699

Asia WGS AF: 0.821 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2100807; hg19: chr3-116023990;