chr3-183153954-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014398.4(LAMP3):c.487A>G(p.Ser163Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014398.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP3 | NM_014398.4 | c.487A>G | p.Ser163Gly | missense_variant | 2/6 | ENST00000265598.8 | |
LAMP3 | XM_005247360.6 | c.487A>G | p.Ser163Gly | missense_variant | 3/7 | ||
LAMP3 | XM_047447967.1 | c.487A>G | p.Ser163Gly | missense_variant | 2/6 | ||
LAMP3 | XM_011512688.3 | c.487A>G | p.Ser163Gly | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP3 | ENST00000265598.8 | c.487A>G | p.Ser163Gly | missense_variant | 2/6 | 1 | NM_014398.4 | P2 | |
LAMP3 | ENST00000466939.1 | c.415A>G | p.Ser139Gly | missense_variant | 2/6 | 2 | A2 | ||
LAMP3 | ENST00000476015.1 | c.487A>G | p.Ser163Gly | missense_variant | 3/3 | 4 | |||
LAMP3 | ENST00000470251.1 | c.415A>G | p.Ser139Gly | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251488Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.487A>G (p.S163G) alteration is located in exon 2 (coding exon 2) of the LAMP3 gene. This alteration results from a A to G substitution at nucleotide position 487, causing the serine (S) at amino acid position 163 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at