chr3-183152030-G-A

Variant names:

• chr3-183152030-G-A
• rs683395
• NM_014398.4:c.888+345C>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+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
• Publications: 20 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=-0.81).
• 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 rank	MANE	Protein	UniProt
LAMP3	NM_014398.4	c.888+345C>T		intron_variant	Intron 3 of 5	ENST00000265598.8	NP_055213.2
LAMP3	XM_005247360.6	c.888+345C>T		intron_variant	Intron 4 of 6		XP_005247417.1
LAMP3	XM_047447967.1	c.888+345C>T		intron_variant	Intron 3 of 5		XP_047303923.1
LAMP3	XM_011512688.3	c.888+345C>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+345C>T		intron_variant	Intron 3 of 5	1	NM_014398.4	ENSP00000265598.3
LAMP3	ENST00000466939.1	c.816+345C>T		intron_variant	Intron 3 of 5	2		ENSP00000418912.1

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

African (AFR) AF: 0.816 AC: 33870 AN: 41496

American (AMR) AF: 0.869 AC: 13283 AN: 15284

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

East Asian (EAS) AF: 0.898 AC: 4641 AN: 5170

South Asian (SAS) AF: 0.879 AC: 4237 AN: 4818

European-Finnish (FIN) AF: 0.916 AC: 9715 AN: 10608

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

European-Non Finnish (NFE) AF: 0.907 AC: 61670 AN: 68010

Other (OTH) AF: 0.888 AC: 1880 AN: 2116

Alfa AF: 0.898 Hom.: 283536

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
PhyloP100		0.054
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: rs683395; hg19: chr3-182869818;