rs1920191

Variant names:

• chr3-116323558-A-G
• rs1920191
• NM_002338.5:c.155+121319T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-116323558-A-G
• chr3-116323558-A-T

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+121319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,062 control chromosomes in the GnomAD database, including 46,931 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 0.78 (46931 hom., cov: 32)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• 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]

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.155+121319T>C		intron_variant	Intron 1 of 6	ENST00000490035.7	NP_002329.2
LSAMP	NM_001318915.2	c.155+121319T>C		intron_variant	Intron 1 of 8		NP_001305844.1
LSAMP	XM_017006383.3	c.155+121319T>C		intron_variant	Intron 1 of 7		XP_016861872.1
LSAMP	XM_011512840.4	c.155+121319T>C		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+121319T>C		intron_variant	Intron 1 of 6	1	NM_002338.5	ENSP00000419000.1

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118795 AN: 151944 Hom.: 46877 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.782 AC: 118898 AN: 152062 Hom.: 46931 Cov.: 32 AF XY: 0.778 AC XY: 57851 AN XY: 74324

African (AFR) AF: 0.868 AC: 36062 AN: 41542

American (AMR) AF: 0.705 AC: 10769 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2523 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4441 AN: 5164

South Asian (SAS) AF: 0.837 AC: 4038 AN: 4822

European-Finnish (FIN) AF: 0.676 AC: 7153 AN: 10582

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.756 AC: 51349 AN: 67904

Other (OTH) AF: 0.789 AC: 1665 AN: 2110

Alfa AF: 0.761 Hom.: 5172

Bravo AF: 0.787

Asia WGS AF: 0.826 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.20
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: rs1920191; hg19: chr3-116042405;