chr3-183151207-G-A

Variant names:

• chr3-183151207-G-A
• rs589445
• NM_014398.4:c.888+1168C>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+1168C>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 152,122 control chromosomes in the GnomAD database, including 58,659 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 (58659 hom., cov: 31)
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 6 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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014398.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	NM_014398.4	MANE Select	c.888+1168C>T		intron	N/A	NP_055213.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	ENST00000265598.8	TSL:1 MANE Select	c.888+1168C>T		intron	N/A	ENSP00000265598.3	Q9UQV4
	LAMP3	ENST00000948307.1		c.888+1168C>T		intron	N/A	ENSP00000618366.1
	LAMP3	ENST00000466939.1	TSL:2	c.816+1168C>T		intron	N/A	ENSP00000418912.1	E7ETP9

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133377 AN: 152004 Hom.: 58627 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: 133464 AN: 152122 Hom.: 58659 Cov.: 31 AF XY: 0.878 AC XY: 65289 AN XY: 74366

African (AFR) AF: 0.816 AC: 33859 AN: 41480

American (AMR) AF: 0.869 AC: 13278 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3077 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4617 AN: 5146

South Asian (SAS) AF: 0.879 AC: 4243 AN: 4828

European-Finnish (FIN) AF: 0.916 AC: 9707 AN: 10596

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

European-Non Finnish (NFE) AF: 0.907 AC: 61663 AN: 68006

Other (OTH) AF: 0.889 AC: 1879 AN: 2114

Alfa AF: 0.887 Hom.: 10431

Bravo AF: 0.872

Asia WGS AF: 0.878 AC: 3052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.4
DANN	Benign	0.81
PhyloP100		-0.95
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: rs589445; hg19: chr3-182868995;