3-183135882-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014398.4(LAMP3):āc.952A>Gā(p.Ile318Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,611,228 control chromosomes in the GnomAD database, including 403,688 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_014398.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP3 | NM_014398.4 | c.952A>G | p.Ile318Val | missense_variant | Exon 5 of 6 | ENST00000265598.8 | NP_055213.2 | |
LAMP3 | XM_005247360.6 | c.952A>G | p.Ile318Val | missense_variant | Exon 6 of 7 | XP_005247417.1 | ||
LAMP3 | XM_047447967.1 | c.1058A>G | p.Asn353Ser | missense_variant | Exon 6 of 6 | XP_047303923.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.589 AC: 89469AN: 151892Hom.: 29369 Cov.: 31
GnomAD3 exomes AF: 0.649 AC: 163032AN: 251102Hom.: 55378 AF XY: 0.666 AC XY: 90356AN XY: 135710
GnomAD4 exome AF: 0.709 AC: 1035093AN: 1459218Hom.: 374334 Cov.: 34 AF XY: 0.711 AC XY: 516276AN XY: 726032
GnomAD4 genome AF: 0.589 AC: 89477AN: 152010Hom.: 29354 Cov.: 31 AF XY: 0.589 AC XY: 43767AN XY: 74318
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at