6-160531806-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005577.4(LPA):c.6046C>T(p.Arg2016Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,613,340 control chromosomes in the GnomAD database, including 57,872 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_005577.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.247 AC: 37469AN: 151880Hom.: 4844 Cov.: 32
GnomAD3 exomes AF: 0.237 AC: 59707AN: 251420Hom.: 7775 AF XY: 0.240 AC XY: 32576AN XY: 135882
GnomAD4 exome AF: 0.265 AC: 387733AN: 1461342Hom.: 53030 Cov.: 36 AF XY: 0.264 AC XY: 191978AN XY: 726984
GnomAD4 genome AF: 0.246 AC: 37467AN: 151998Hom.: 4842 Cov.: 32 AF XY: 0.245 AC XY: 18164AN XY: 74278
ClinVar
Submissions by phenotype
not provided Benign:1
This variant is associated with the following publications: (PMID: 30389748) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at