XR_924361.3:n.30064-8645C>T

Variant names:

• chr3-117524949-C-T
• rs72951640
• ENST00000717962.1:n.536-185162G>A

Variant summary

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

The XR_924361.3(LOC105374056):​n.30064-8645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,264 control chromosomes in the GnomAD database, including 280 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 0.045 (280 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 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]

ENSG00000303790 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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	ENST00000717962.1		n.536-185162G>A		intron	N/A
	ENSG00000303790	ENST00000797238.1		n.157-8645C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6874 AN: 152146 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0452 AC: 6881 AN: 152264 Hom.: 280 Cov.: 32 AF XY: 0.0453 AC XY: 3370 AN XY: 74468

African (AFR) AF: 0.109 AC: 4521 AN: 41526

American (AMR) AF: 0.0243 AC: 372 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.0946 AC: 491 AN: 5188

South Asian (SAS) AF: 0.0437 AC: 211 AN: 4828

European-Finnish (FIN) AF: 0.0109 AC: 116 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0143 AC: 972 AN: 68024

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0280 Hom.: 38

Bravo AF: 0.0498

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.33
DANN	Benign	0.35
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs72951640; hg19: chr3-117243796;