chr6:160585140-T>G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000316300.10(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 0.129 in 1,613,538 control chromosomes in the GnomAD database, including 14,785 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.
Frequency
Consequence
ENST00000316300.10 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPA | NM_005577.4 | c.4195A>C | p.Thr1399Pro | missense_variant | 26/39 | ENST00000316300.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPA | ENST00000316300.10 | c.4195A>C | p.Thr1399Pro | missense_variant | 26/39 | 1 | NM_005577.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0990 AC: 15048AN: 152070Hom.: 949 Cov.: 32
GnomAD3 exomes AF: 0.110 AC: 27534AN: 250654Hom.: 1883 AF XY: 0.113 AC XY: 15278AN XY: 135758
GnomAD4 exome AF: 0.132 AC: 192617AN: 1461350Hom.: 13836 Cov.: 33 AF XY: 0.131 AC XY: 95584AN XY: 727010
GnomAD4 genome ? AF: 0.0989 AC: 15053AN: 152188Hom.: 949 Cov.: 32 AF XY: 0.0976 AC XY: 7265AN XY: 74422
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at