Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005577(LPA):c.4195A>C(p.Thr1399Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152070 control chromosomes in the gnomAD Genomes database, including 949 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/16 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 same amino acid change has been previously reported as Likely benignin UniProt.
Verdict is Benign. Variant got -12 ACMG points.
GnomAD3 genomes AF: 0.0990AC: 15048AN: 152070Hom.: 949Cov.: 32 GnomAD3 exomes AF: 0.110AC: 27534AN: 250654Hom.: 1883 AF XY: 0.113AC XY: 15278AN XY: 135758 GnomAD4 exome AF: 0.132AC: 192617AN: 1461350Hom.: 13836 AF XY: 0.131AC XY: 95584AN XY: 727010
ClinVarNot reported in
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