rs1521417

chr3-117042266-A-G

Variant summary

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

The XR_007096015.1(LOC124909415):n.29330-32892T>C 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 0.57 in 152,024 control chromosomes in the GnomAD database, including 25,969 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 0.57 (25969 hom., cov: 32)
• Consequence: LOC124909415 XR_007096015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909415	XR_007096015.1	n.29330-32892T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000474851.1	c.34-32892T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86559 AN: 151906 Hom.: 25969 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.570 AC: 86587 AN: 152024 Hom.: 25969 Cov.: 32 AF XY: 0.560 AC XY: 41630 AN XY: 74320

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.609

Alfa AF: 0.587 Hom.: 3911

Bravo AF: 0.570

Asia WGS AF: 0.430 AC: 1496 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.6
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1521417; hg19: chr3-116761113;