rs10513791

Variant names:

• chr3-183145188-G-T
• rs10513791
• NM_014398.4:c.889-4593C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.96).
• 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 rank	MANE	Protein	UniProt
LAMP3	NM_014398.4	c.889-4593C>A		intron_variant	Intron 3 of 5	ENST00000265598.8	NP_055213.2
LAMP3	XM_005247360.6	c.889-4593C>A		intron_variant	Intron 4 of 6		XP_005247417.1
LAMP3	XM_047447967.1	c.889-4593C>A		intron_variant	Intron 3 of 5		XP_047303923.1
LAMP3	XM_011512688.3	c.889-4593C>A		intron_variant	Intron 3 of 5		XP_011510990.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMP3	ENST00000265598.8	c.889-4593C>A		intron_variant	Intron 3 of 5	1	NM_014398.4	ENSP00000265598.3
LAMP3	ENST00000466939.1	c.817-4593C>A		intron_variant	Intron 3 of 5	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

African (AFR) AF: 0.0490 AC: 2035 AN: 41544

American (AMR) AF: 0.0635 AC: 971 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0664 AC: 230 AN: 3466

East Asian (EAS) AF: 0.163 AC: 840 AN: 5164

South Asian (SAS) AF: 0.111 AC: 536 AN: 4822

European-Finnish (FIN) AF: 0.0964 AC: 1022 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5300 AN: 68006

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0766 Hom.: 712

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
PhyloP100		0.50
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: rs10513791; hg19: chr3-182862976;