chr3-117510933-A-G

Variant names:

• chr3-117510933-A-G
• rs1875518
• XR_007096021.1:n.27613A>G

Variant summary

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

The XR_007096021.1(LOC105374056):​n.27613A>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 0.403 in 152,090 control chromosomes in the GnomAD database, including 15,044 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 (15044 hom., cov: 32)
• Consequence: LOC105374056 XR_007096021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374056	XR_007096021.1	n.27613A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105374056	XR_924361.3	n.27613A>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.536-171146T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61352 AN: 151972 Hom.: 15052 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.403 AC: 61325 AN: 152090 Hom.: 15044 Cov.: 32 AF XY: 0.399 AC XY: 29683 AN XY: 74334

African (AFR) AF: 0.128 AC: 5326 AN: 41518

American (AMR) AF: 0.360 AC: 5495 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1547 AN: 5176

South Asian (SAS) AF: 0.448 AC: 2161 AN: 4824

European-Finnish (FIN) AF: 0.497 AC: 5241 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38345 AN: 67956

Other (OTH) AF: 0.417 AC: 883 AN: 2116

Alfa AF: 0.460 Hom.: 2401

Bravo AF: 0.377

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.87
PhyloP100		1.1
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: rs1875518; hg19: chr3-117229780;