3-116442687-T-A

Position:

• chr3-116442687-T-A

Variant summary

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

The NM_002338.5(LSAMP):​c.155+2190A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,030 control chromosomes in the GnomAD database, including 24,615 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 (24615 hom., cov: 32)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.155+2190A>T		intron_variant		ENST00000490035.7	NP_002329.2
LSAMP	NM_001318915.2	c.155+2190A>T		intron_variant			NP_001305844.1
LSAMP	XM_011512840.4	c.155+2190A>T		intron_variant			XP_011511142.1
LSAMP	XM_017006383.3	c.155+2190A>T		intron_variant			XP_016861872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000490035.7	c.155+2190A>T		intron_variant		1	NM_002338.5	ENSP00000419000	P1
LSAMP	ENST00000333617.8	c.107+2190A>T		intron_variant		2		ENSP00000328455
LSAMP	ENST00000474851.1	c.257+2190A>T		intron_variant		5		ENSP00000418506

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81230 AN: 151910 Hom.: 24624 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.534 AC: 81218 AN: 152030 Hom.: 24615 Cov.: 32 AF XY: 0.538 AC XY: 39957 AN XY: 74306

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.574

Alfa AF: 0.447 Hom.: 1405

Bravo AF: 0.519

Asia WGS AF: 0.652 AC: 2269 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	9.1
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9822445; hg19: chr3-116161534;