rs45458507

Variant names:

• chr3-117497574-A-G
• rs45458507
• XR_007096021.1:n.14254A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-117497574-A-G
• chr3-117497574-A-T

Variant summary

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

The XR_007096021.1(LOC105374056):​n.14254A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 152,308 control chromosomes in the GnomAD database, including 279 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 0.056 (279 hom., cov: 32)
• Consequence: LOC105374056 XR_007096021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

Genes affected

LOC105374056 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374056	XR_007096021.1	n.14254A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105374056	XR_924361.3	n.14254A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000717962.1	n.536-157787T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8531 AN: 152188 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0561 AC: 8541 AN: 152308 Hom.: 279 Cov.: 32 AF XY: 0.0554 AC XY: 4127 AN XY: 74478

African (AFR) AF: 0.0287 AC: 1195 AN: 41572

American (AMR) AF: 0.0568 AC: 868 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5192

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4828

European-Finnish (FIN) AF: 0.0573 AC: 608 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4783 AN: 68012

Other (OTH) AF: 0.0761 AC: 161 AN: 2116

Alfa AF: 0.0502 Hom.: 93

Bravo AF: 0.0535

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.59
PhyloP100		-1.2
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: rs45458507; hg19: chr3-117216421;