3-116772825-C-T

Variant names:

• chr3-116772825-C-T
• rs1835856
• ENST00000474851.1:c.178+236405G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717962.1(LSAMP):​n.686+236457G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,988 control chromosomes in the GnomAD database, including 3,067 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 0.20 (3067 hom., cov: 32)
• Consequence: LSAMP ENST00000717962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 1 publications found

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]

ENSG00000296097 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSAMP	ENST00000474851.1	TSL:5	c.178+236405G>A		intron	N/A	ENSP00000418506.1	C9J5G3
	LSAMP	ENST00000717962.1		n.686+236457G>A		intron	N/A
	ENSG00000296097	ENST00000736393.1		n.87+208G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29865 AN: 151870 Hom.: 3063 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.197 AC: 29889 AN: 151988 Hom.: 3067 Cov.: 32 AF XY: 0.195 AC XY: 14470 AN XY: 74282

African (AFR) AF: 0.268 AC: 11115 AN: 41422

American (AMR) AF: 0.151 AC: 2312 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3468

East Asian (EAS) AF: 0.185 AC: 956 AN: 5178

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1713 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11144 AN: 67964

Other (OTH) AF: 0.219 AC: 461 AN: 2106

Alfa AF: 0.177 Hom.: 1276

Bravo AF: 0.198

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.60
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1835856;

hg19: chr3-116491672;