chr13-113306530-G-A
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005561.4(LAMP1):c.107G>A(p.Gly36Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000725 in 1,614,076 control chromosomes in the GnomAD database, including 15 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_005561.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP1 | NM_005561.4 | c.107G>A | p.Gly36Asp | missense_variant | Exon 2 of 9 | ENST00000332556.5 | NP_005552.3 | |
LAMP1 | XM_011537494.3 | c.50G>A | p.Gly17Asp | missense_variant | Exon 2 of 9 | XP_011535796.1 | ||
LAMP1 | XM_047430302.1 | c.41G>A | p.Gly14Asp | missense_variant | Exon 2 of 9 | XP_047286258.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000907 AC: 138AN: 152134Hom.: 2 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00222 AC: 555AN: 249548 AF XY: 0.00197 show subpopulations
GnomAD4 exome AF: 0.000707 AC: 1033AN: 1461824Hom.: 13 Cov.: 31 AF XY: 0.000652 AC XY: 474AN XY: 727216 show subpopulations
GnomAD4 genome AF: 0.000906 AC: 138AN: 152252Hom.: 2 Cov.: 31 AF XY: 0.00102 AC XY: 76AN XY: 74440 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at