rs10511364

chr3-117119049-A-C

Variant summary

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

The XR_007096015.1(LOC124909415):n.29330-109675T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,152 control chromosomes in the GnomAD database, including 403 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 0.048 (403 hom., cov: 32)
• Consequence: LOC124909415 XR_007096015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

LOC124909415 (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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909415	XR_007096015.1	n.29330-109675T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000474851.1	c.33+20152T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7229 AN: 152034 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00919

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0476 AC: 7240 AN: 152152 Hom.: 403 Cov.: 32 AF XY: 0.0511 AC XY: 3802 AN XY: 74388

Gnomad4 AFR AF: 0.0829

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00919

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0272 Hom.: 39

Bravo AF: 0.0529

Asia WGS AF: 0.188 AC: 652 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511364; hg19: chr3-116837896;