rs1609970

chr3-116915449-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000474851.1(LSAMP):c.178+93781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,092 control chromosomes in the GnomAD database, including 2,662 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 0.14 (2662 hom., cov: 32)
• Consequence: LSAMP ENST00000474851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000474851.1	c.178+93781G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21898 AN: 151974 Hom.: 2660 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.144 AC: 21926 AN: 152092 Hom.: 2662 Cov.: 32 AF XY: 0.139 AC XY: 10334 AN XY: 74334

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.120

Alfa AF: 0.104 Hom.: 293

Bravo AF: 0.156

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.9
Dann	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1609970; hg19: chr3-116634296;