rs876657484
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002294.3(LAMP2):āc.657A>Gā(p.Glu219=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000894 in 111,854 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002294.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.657A>G | p.Glu219= | synonymous_variant | 5/9 | ENST00000200639.9 | |
LAMP2 | NM_001122606.1 | c.657A>G | p.Glu219= | synonymous_variant | 5/9 | ||
LAMP2 | NM_013995.2 | c.657A>G | p.Glu219= | synonymous_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.657A>G | p.Glu219= | synonymous_variant | 5/9 | 1 | NM_002294.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111854Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34006
GnomAD4 exome Cov.: 29
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111854Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34006
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 26, 2015 | p.Glu219Glu in exon 5 of LAMP2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at