3-117501497-C-T

Variant names:

• chr3-117501497-C-T
• rs2055426
• XR_007096021.1:n.18177C>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.18177C>T 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 0.395 in 151,764 control chromosomes in the GnomAD database, including 14,558 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 (14558 hom., cov: 31)
• Consequence: LOC105374056 XR_007096021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374056	XR_007096021.1	n.18177C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105374056	XR_924361.3	n.18177C>T		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.536-161710G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59990 AN: 151646 Hom.: 14563 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.395 AC: 59964 AN: 151764 Hom.: 14558 Cov.: 31 AF XY: 0.390 AC XY: 28907 AN XY: 74170

African (AFR) AF: 0.128 AC: 5282 AN: 41406

American (AMR) AF: 0.330 AC: 5019 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1788 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1147 AN: 5166

South Asian (SAS) AF: 0.444 AC: 2132 AN: 4804

European-Finnish (FIN) AF: 0.498 AC: 5223 AN: 10496

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

European-Non Finnish (NFE) AF: 0.560 AC: 38021 AN: 67882

Other (OTH) AF: 0.409 AC: 860 AN: 2104

Alfa AF: 0.513 Hom.: 10901

Bravo AF: 0.367

Asia WGS AF: 0.321 AC: 1118 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.49
PhyloP100		0.091
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: rs2055426; hg19: chr3-117220344;