chr3-116366831-A-T

Variant names:

• chr3-116366831-A-T
• rs988803
• NM_002338.5:c.155+78046T>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+78046T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,002 control chromosomes in the GnomAD database, including 54,140 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 0.84 (54140 hom., cov: 30)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.17
• Publications: 5 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002338.5. 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
	LSAMP	NM_002338.5	MANE Select	c.155+78046T>A		intron	N/A	NP_002329.2
	LSAMP	NM_001318915.2		c.155+78046T>A		intron	N/A	NP_001305844.1
	LSAMP-AS1	NR_109998.1		n.71-1111A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000490035.7	TSL:1 MANE Select	c.155+78046T>A		intron	N/A	ENSP00000419000.1	Q13449
	LSAMP	ENST00000333617.8	TSL:2	c.107+78046T>A		intron	N/A	ENSP00000328455.4	H3BLU2
	LSAMP	ENST00000474851.1	TSL:5	c.257+78046T>A		intron	N/A	ENSP00000418506.1	C9J5G3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127850 AN: 151886 Hom.: 54096 Cov.: 30

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.842 AC: 127942 AN: 152002 Hom.: 54140 Cov.: 30 AF XY: 0.837 AC XY: 62215 AN XY: 74298

African (AFR) AF: 0.886 AC: 36730 AN: 41464

American (AMR) AF: 0.802 AC: 12225 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4878 AN: 5164

South Asian (SAS) AF: 0.927 AC: 4463 AN: 4816

European-Finnish (FIN) AF: 0.708 AC: 7456 AN: 10538

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.829 AC: 56394 AN: 67986

Other (OTH) AF: 0.860 AC: 1815 AN: 2110

Alfa AF: 0.756 Hom.: 2187

Bravo AF: 0.849

Asia WGS AF: 0.906 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.042
DANN	Benign	0.15
PhyloP100		-5.2
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: rs988803; hg19: chr3-116085678;