rs938911

Variant names:

• chr3-116701355-A-G
• rs938911
• ENST00000474851.1:c.179-256400T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000474851.1(LSAMP):​c.179-256400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,108 control chromosomes in the GnomAD database, including 3,250 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 0.19 (3250 hom., cov: 32)
• Consequence: LSAMP ENST00000474851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000474851.1	c.179-256400T>C		intron_variant	Intron 2 of 4	5		ENSP00000418506.1
LSAMP	ENST00000717962.1	n.687-256400T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28862 AN: 151990 Hom.: 3240 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.190 AC: 28901 AN: 152108 Hom.: 3250 Cov.: 32 AF XY: 0.186 AC XY: 13825 AN XY: 74378

African (AFR) AF: 0.316 AC: 13113 AN: 41462

American (AMR) AF: 0.108 AC: 1646 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.116 AC: 602 AN: 5170

South Asian (SAS) AF: 0.183 AC: 883 AN: 4828

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10602

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10132 AN: 67974

Other (OTH) AF: 0.176 AC: 371 AN: 2106

Alfa AF: 0.155 Hom.: 2406

Bravo AF: 0.189

Asia WGS AF: 0.171 AC: 592 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		0.85
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: rs938911; hg19: chr3-116420202;