rs10513791

Positions:

• chr3-183145188-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.889-4593C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 152,210 control chromosomes in the GnomAD database, including 467 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 0.074 (467 hom., cov: 32)
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMP3	NM_014398.4	c.889-4593C>A		intron_variant		ENST00000265598.8	NP_055213.2
LAMP3	XM_005247360.6	c.889-4593C>A		intron_variant			XP_005247417.1
LAMP3	XM_047447967.1	c.889-4593C>A		intron_variant			XP_047303923.1
LAMP3	XM_011512688.3	c.889-4593C>A		intron_variant			XP_011510990.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAMP3	ENST00000265598.8	c.889-4593C>A		intron_variant		1	NM_014398.4	ENSP00000265598.3
LAMP3	ENST00000466939.1	c.817-4593C>A		intron_variant		2		ENSP00000418912.1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11227 AN: 152092 Hom.: 469 Cov.: 32

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0664

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0738 AC: 11228 AN: 152210 Hom.: 467 Cov.: 32 AF XY: 0.0744 AC XY: 5534 AN XY: 74400

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.0635

Gnomad4 ASJ AF: 0.0664

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0780 Hom.: 610

Bravo AF: 0.0708

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.36

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: rs10513791; hg19: chr3-182862976;