chr13-113309730-G-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005561.4(LAMP1):c.271G>A(p.Val91Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005561.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP1 | NM_005561.4 | c.271G>A | p.Val91Met | missense_variant | Exon 3 of 9 | ENST00000332556.5 | NP_005552.3 | |
LAMP1 | XM_011537494.3 | c.214G>A | p.Val72Met | missense_variant | Exon 3 of 9 | XP_011535796.1 | ||
LAMP1 | XM_047430302.1 | c.205G>A | p.Val69Met | missense_variant | Exon 3 of 9 | XP_047286258.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000120 AC: 3AN: 249578 AF XY: 0.0000222 show subpopulations
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727236 show subpopulations
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.271G>A (p.V91M) alteration is located in exon 3 (coding exon 3) of the LAMP1 gene. This alteration results from a G to A substitution at nucleotide position 271, causing the valine (V) at amino acid position 91 to be replaced by a methionine (M). 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