3-183154050-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_014398.4(LAMP3):c.391C>T(p.Pro131Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,028 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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
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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.391C>T | p.Pro131Ser | missense_variant | 2/6 | ENST00000265598.8 | |
LAMP3 | XM_005247360.6 | c.391C>T | p.Pro131Ser | missense_variant | 3/7 | ||
LAMP3 | XM_047447967.1 | c.391C>T | p.Pro131Ser | missense_variant | 2/6 | ||
LAMP3 | XM_011512688.3 | c.391C>T | p.Pro131Ser | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP3 | ENST00000265598.8 | c.391C>T | p.Pro131Ser | missense_variant | 2/6 | 1 | NM_014398.4 | P2 | |
LAMP3 | ENST00000466939.1 | c.319C>T | p.Pro107Ser | missense_variant | 2/6 | 2 | A2 | ||
LAMP3 | ENST00000476015.1 | c.391C>T | p.Pro131Ser | missense_variant | 3/3 | 4 | |||
LAMP3 | ENST00000470251.1 | c.319C>T | p.Pro107Ser | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251436Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135892
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461886Hom.: 3 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.391C>T (p.P131S) alteration is located in exon 2 (coding exon 2) of the LAMP3 gene. This alteration results from a C to T substitution at nucleotide position 391, causing the proline (P) at amino acid position 131 to be replaced by a serine (S). 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