chr3-183152648-G-C

Variant names:

• chr3-183152648-G-C
• rs514636
• NM_014398.4:c.760-145C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014398.4(LAMP3):​c.760-145C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LAMP3 NM_014398.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 18 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	NM_014398.4	MANE Select	c.760-145C>G		intron	N/A	NP_055213.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMP3	ENST00000265598.8	TSL:1 MANE Select	c.760-145C>G		intron	N/A	ENSP00000265598.3
	LAMP3	ENST00000948307.1		c.760-145C>G		intron	N/A	ENSP00000618366.1
	LAMP3	ENST00000466939.1	TSL:2	c.688-145C>G		intron	N/A	ENSP00000418912.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000212 AC: 1 AN: 470816 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 247144

African (AFR) AF: 0.00 AC: 0 AN: 11778

American (AMR) AF: 0.00 AC: 0 AN: 18698

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12438

East Asian (EAS) AF: 0.00 AC: 0 AN: 28940

South Asian (SAS) AF: 0.00 AC: 0 AN: 32306

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33142

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1850

European-Non Finnish (NFE) AF: 0.00000327 AC: 1 AN: 306258

Other (OTH) AF: 0.00 AC: 0 AN: 25406

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 189578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.50
PhyloP100		0.078

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: rs514636; hg19: chr3-182870436;