rs9810432

chr3-117109120-C-T

Variant summary

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

The XR_007096015.1(LOC124909415):n.29330-99746G>A 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 0.527 in 151,884 control chromosomes in the GnomAD database, including 21,201 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 0.53 (21201 hom., cov: 31)
• Consequence: LOC124909415 XR_007096015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909415	XR_007096015.1	n.29330-99746G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSAMP	ENST00000474851.1	c.33+30081G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80008 AN: 151766 Hom.: 21185 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.527 AC: 80077 AN: 151884 Hom.: 21201 Cov.: 31 AF XY: 0.526 AC XY: 39063 AN XY: 74224

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.543

Alfa AF: 0.517 Hom.: 26872

Bravo AF: 0.536

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.9
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9810432; hg19: chr3-116827967;