3-115819804-G-C

Position:

• chr3-115819804-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002338.5(LSAMP):​c.920-9390C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,088 control chromosomes in the GnomAD database, including 7,902 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 0.31 (7902 hom., cov: 31)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.920-9390C>G		intron_variant		ENST00000490035.7	NP_002329.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000490035.7	c.920-9390C>G		intron_variant		1	NM_002338.5	ENSP00000419000.1
LSAMP	ENST00000333617.8	c.908-3158C>G		intron_variant		2		ENSP00000328455.4
LSAMP	ENST00000475403.2	n.226-3158C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47578 AN: 151970 Hom.: 7875 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.313 AC: 47646 AN: 152088 Hom.: 7902 Cov.: 31 AF XY: 0.305 AC XY: 22649 AN XY: 74356

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.310

Alfa AF: 0.161 Hom.: 290

Bravo AF: 0.329

Asia WGS AF: 0.187 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.6
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs9822311; hg19: chr3-115538651;