chr3-183152648-G-A

Variant names:

• chr3-183152648-G-A
• rs514636
• NM_014398.4:c.760-145C>T

Variant summary

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

The NM_014398.4(LAMP3):​c.760-145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 622,560 control chromosomes in the GnomAD database, including 248,745 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 0.88 (58672 hom., cov: 32)
  • Exomes 𝑓: 0.90 (190073 hom.)
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 18 publications found

Genes affected

LAMP3 (HGNC:14582): (lysosomal associated membrane protein 3) Dendritic cells (DCs) are the most potent antigen-presenting cells. Immature DCs efficiently capture antigens and differentiate into interdigitating dendritic cells (IDCs) in lymphoid tissues that induce primary T-cell responses (summary by de Saint-Vis et al., 1998 [PubMed 9768752]).[supplied by OMIM, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014398.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	NM_014398.4	MANE Select	c.760-145C>T		intron	N/A	NP_055213.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	ENST00000265598.8	TSL:1 MANE Select	c.760-145C>T		intron	N/A	ENSP00000265598.3
	LAMP3	ENST00000948307.1		c.760-145C>T		intron	N/A	ENSP00000618366.1
	LAMP3	ENST00000466939.1	TSL:2	c.688-145C>T		intron	N/A	ENSP00000418912.1

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133414 AN: 152058 Hom.: 58640 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.889

GnomAD4 exome AF: 0.898 AC: 422488 AN: 470384 Hom.: 190073 AF XY: 0.898 AC XY: 221807 AN XY: 246914

African (AFR) AF: 0.812 AC: 9546 AN: 11756

American (AMR) AF: 0.857 AC: 16016 AN: 18682

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 10992 AN: 12432

East Asian (EAS) AF: 0.900 AC: 26024 AN: 28922

South Asian (SAS) AF: 0.868 AC: 28007 AN: 32254

European-Finnish (FIN) AF: 0.914 AC: 30285 AN: 33120

Middle Eastern (MID) AF: 0.871 AC: 1609 AN: 1848

European-Non Finnish (NFE) AF: 0.906 AC: 277281 AN: 305984

Other (OTH) AF: 0.895 AC: 22728 AN: 25386

GnomAD4 genome AF: 0.877 AC: 133501 AN: 152176 Hom.: 58672 Cov.: 32 AF XY: 0.878 AC XY: 65296 AN XY: 74386

African (AFR) AF: 0.816 AC: 33879 AN: 41506

American (AMR) AF: 0.869 AC: 13291 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3078 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4634 AN: 5162

South Asian (SAS) AF: 0.879 AC: 4237 AN: 4820

European-Finnish (FIN) AF: 0.916 AC: 9699 AN: 10594

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61667 AN: 68016

Other (OTH) AF: 0.889 AC: 1875 AN: 2108

Alfa AF: 0.895 Hom.: 189578

Bravo AF: 0.872

Asia WGS AF: 0.877 AC: 3048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.63
PhyloP100		0.078
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs514636; hg19: chr3-182870436;