rs42890

chrX-120444658-A-CchrX-120444658-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_002294.3(LAMP2):c.864+1647T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (16863 hom., 21176 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LAMP2 NM_002294.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LAMP2 (HGNC:6501): (lysosomal associated membrane protein 2) The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd at 16864 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAMP2	NM_002294.3	c.864+1647T>G		intron_variant		ENST00000200639.9
LAMP2	NM_001122606.1	c.864+1647T>G		intron_variant
LAMP2	NM_013995.2	c.864+1647T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAMP2	ENST00000200639.9	c.864+1647T>G		intron_variant		1	NM_002294.3	P3

Frequencies

GnomAD3 genomes AF: 0.653 AC: 71984 AN: 110276 Hom.: 16864 Cov.: 22 AF XY: 0.649 AC XY: 21116 AN XY: 32536

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.644

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.653 AC: 72036 AN: 110330 Hom.: 16863 Cov.: 22 AF XY: 0.650 AC XY: 21176 AN XY: 32600

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.648

Alfa AF: 0.611 Hom.: 5505

Bravo AF: 0.672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.88
Dann	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs42890; hg19: chrX-119578513;