chr3-183153694-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014398.4(LAMP3):āc.747A>Cā(p.Gln249His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000733 in 1,364,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014398.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP3 | NM_014398.4 | c.747A>C | p.Gln249His | missense_variant | 2/6 | ENST00000265598.8 | |
LAMP3 | XM_005247360.6 | c.747A>C | p.Gln249His | missense_variant | 3/7 | ||
LAMP3 | XM_047447967.1 | c.747A>C | p.Gln249His | missense_variant | 2/6 | ||
LAMP3 | XM_011512688.3 | c.747A>C | p.Gln249His | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP3 | ENST00000265598.8 | c.747A>C | p.Gln249His | missense_variant | 2/6 | 1 | NM_014398.4 | P2 | |
LAMP3 | ENST00000466939.1 | c.675A>C | p.Gln225His | missense_variant | 2/6 | 2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.33e-7 AC: 1AN: 1364930Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 668412
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 2023 | The c.747A>C (p.Q249H) alteration is located in exon 2 (coding exon 2) of the LAMP3 gene. This alteration results from a A to C substitution at nucleotide position 747, causing the glutamine (Q) at amino acid position 249 to be replaced by a histidine (H). 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