chr3-117189985-T-G

Variant names:

• chr3-117189985-T-G
• rs1915585
• ENST00000717962.1:n.593+149745A>C

Variant summary

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

The ENST00000717962.1(LSAMP):​n.593+149745A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 151,670 control chromosomes in the GnomAD database, including 59,911 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 0.89 (59911 hom., cov: 28)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 2 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]

LOC124909415 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909415	XR_007096015.1	n.29329+59031A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000717962.1	n.593+149745A>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.888 AC: 134565 AN: 151552 Hom.: 59847 Cov.: 28

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.888 AC: 134687 AN: 151670 Hom.: 59911 Cov.: 28 AF XY: 0.892 AC XY: 66071 AN XY: 74092

African (AFR) AF: 0.922 AC: 38161 AN: 41388

American (AMR) AF: 0.911 AC: 13811 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3182 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5141 AN: 5156

South Asian (SAS) AF: 0.903 AC: 4342 AN: 4808

European-Finnish (FIN) AF: 0.896 AC: 9423 AN: 10522

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57705 AN: 67848

Other (OTH) AF: 0.889 AC: 1880 AN: 2114

Alfa AF: 0.869 Hom.: 32989

Bravo AF: 0.891

Asia WGS AF: 0.956 AC: 3319 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.61
PhyloP100		-0.68
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: rs1915585; hg19: chr3-116908832;