NM_032802.4:c.67-6659C>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032802.4(SPPL2A):c.67-6659C>A 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: 28)
Consequence
SPPL2A
NM_032802.4 intron
NM_032802.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.511
Publications
12 publications found
Genes affected
SPPL2A (HGNC:30227): (signal peptide peptidase like 2A) This gene encodes a member of the GXGD family of aspartic proteases, which are transmembrane proteins with two conserved catalytic motifs localized within the membrane-spanning regions, as well as a member of the signal peptide peptidase-like protease (SPPL) family. This protein is expressed in all major adult human tissues and localizes to late endosomal compartments and lysosomal membranes. A pseudogene of this gene also lies on chromosome 15. [provided by RefSeq, Feb 2012]
SPPL2A Gene-Disease associations (from GenCC):
- immunodeficiency 86Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
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=-0.94).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPPL2A | NM_032802.4 | c.67-6659C>A | intron_variant | Intron 1 of 14 | ENST00000261854.10 | NP_116191.2 | ||
SPPL2A | NM_001438111.1 | c.67-6659C>A | intron_variant | Intron 1 of 15 | NP_001425040.1 | |||
SPPL2A | NM_001438112.1 | c.67-6659C>A | intron_variant | Intron 1 of 13 | NP_001425041.1 | |||
SPPL2A | XM_017022680.2 | c.67-6659C>A | intron_variant | Intron 1 of 14 | XP_016878169.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
Cov.:
28
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 28
GnomAD4 genome
Cov.:
28
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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