chr6-160586506-G-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005577.4(LPA):āc.4072C>Gā(p.Leu1358Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,613,150 control chromosomes in the GnomAD database, including 103,992 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 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
NM_005577.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPA | NM_005577.4 | c.4072C>G | p.Leu1358Val | missense_variant | 25/39 | ENST00000316300.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPA | ENST00000316300.10 | c.4072C>G | p.Leu1358Val | missense_variant | 25/39 | 1 | NM_005577.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.405 AC: 61511AN: 151940Hom.: 13206 Cov.: 32
GnomAD3 exomes AF: 0.353 AC: 88052AN: 249370Hom.: 16264 AF XY: 0.355 AC XY: 48028AN XY: 135272
GnomAD4 exome AF: 0.348 AC: 508819AN: 1461092Hom.: 90756 Cov.: 51 AF XY: 0.349 AC XY: 253736AN XY: 726868
GnomAD4 genome AF: 0.405 AC: 61603AN: 152058Hom.: 13236 Cov.: 32 AF XY: 0.404 AC XY: 30048AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at