rs683395

Positions:

• chr3-183152030-G-A
• chr3-183152030-G-C
• chr3-183152030-G-T

Variant summary

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

The NM_014398.4(LAMP3):​c.888+345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,180 control chromosomes in the GnomAD database, including 58,685 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 (58685 hom., cov: 31)
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAMP3	NM_014398.4	c.888+345C>T		intron_variant		ENST00000265598.8
LAMP3	XM_005247360.6	c.888+345C>T		intron_variant
LAMP3	XM_011512688.3	c.888+345C>T		intron_variant
LAMP3	XM_047447967.1	c.888+345C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAMP3	ENST00000265598.8	c.888+345C>T		intron_variant		1	NM_014398.4	P2
LAMP3	ENST00000466939.1	c.816+345C>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133428 AN: 152062 Hom.: 58653 Cov.: 31

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: 0.888

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

GnomAD4 genome AF: 0.877 AC: 133515 AN: 152180 Hom.: 58685 Cov.: 31 AF XY: 0.878 AC XY: 65341 AN XY: 74428

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.888

Alfa AF: 0.901 Hom.: 139827

Bravo AF: 0.872

Asia WGS AF: 0.878 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.74

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: rs683395; hg19: chr3-182869818;