chr3-117513540-A-G

Variant names:

• chr3-117513540-A-G
• rs2937673
• ENST00000717962.1:n.536-173753T>C

Variant summary

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

The ENST00000717962.1(LSAMP):​n.536-173753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,986 control chromosomes in the GnomAD database, including 14,789 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 0.40 (14789 hom., cov: 31)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27
• 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]

ENSG00000303790 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717962.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000717962.1		n.536-173753T>C		intron	N/A
	ENSG00000303790	ENST00000797238.1		n.116+197A>G		intron	N/A
	ENSG00000303790	ENST00000797242.1		n.148+197A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60481 AN: 151870 Hom.: 14794 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.398 AC: 60458 AN: 151986 Hom.: 14789 Cov.: 31 AF XY: 0.392 AC XY: 29137 AN XY: 74270

African (AFR) AF: 0.128 AC: 5321 AN: 41498

American (AMR) AF: 0.332 AC: 5055 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1791 AN: 3462

East Asian (EAS) AF: 0.225 AC: 1160 AN: 5160

South Asian (SAS) AF: 0.449 AC: 2164 AN: 4818

European-Finnish (FIN) AF: 0.498 AC: 5249 AN: 10548

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38349 AN: 67934

Other (OTH) AF: 0.413 AC: 874 AN: 2114

Alfa AF: 0.402 Hom.: 8316

Bravo AF: 0.370

Asia WGS AF: 0.325 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		2.3
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: rs2937673; hg19: chr3-117232387;