rs12493050

Variant names:

• chr3-183147285-G-A
• rs12493050
• NM_014398.4:c.888+5090C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-183147285-G-A
• chr3-183147285-G-C
• chr3-183147285-G-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.888+5090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 151,860 control chromosomes in the GnomAD database, including 42,736 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 0.75 (42736 hom., cov: 29)
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMP3	NM_014398.4	c.888+5090C>T		intron_variant	Intron 3 of 5	ENST00000265598.8	NP_055213.2
LAMP3	XM_005247360.6	c.888+5090C>T		intron_variant	Intron 4 of 6		XP_005247417.1
LAMP3	XM_047447967.1	c.888+5090C>T		intron_variant	Intron 3 of 5		XP_047303923.1
LAMP3	XM_011512688.3	c.888+5090C>T		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.888+5090C>T		intron_variant	Intron 3 of 5	1	NM_014398.4	ENSP00000265598.3
LAMP3	ENST00000466939.1	c.816+5090C>T		intron_variant	Intron 3 of 5	2		ENSP00000418912.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113392 AN: 151740 Hom.: 42714 Cov.: 29

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.747 AC: 113475 AN: 151860 Hom.: 42736 Cov.: 29 AF XY: 0.749 AC XY: 55606 AN XY: 74226

African (AFR) AF: 0.647 AC: 26749 AN: 41358

American (AMR) AF: 0.766 AC: 11704 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2619 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3781 AN: 5158

South Asian (SAS) AF: 0.757 AC: 3644 AN: 4812

European-Finnish (FIN) AF: 0.798 AC: 8395 AN: 10524

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54097 AN: 67952

Other (OTH) AF: 0.753 AC: 1585 AN: 2106

Alfa AF: 0.784 Hom.: 39487

Bravo AF: 0.740

Asia WGS AF: 0.767 AC: 2666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.34
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: rs12493050; hg19: chr3-182865073;