6-160540105-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_005577.4(LPA):āc.5673A>Gā(p.Ile1891Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 1,614,110 control chromosomes in the GnomAD database, including 2,565 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_005577.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0321 AC: 4885AN: 152100Hom.: 296 Cov.: 32
GnomAD3 exomes AF: 0.0557 AC: 14019AN: 251472Hom.: 1639 AF XY: 0.0455 AC XY: 6190AN XY: 135910
GnomAD4 exome AF: 0.0268 AC: 39248AN: 1461892Hom.: 2259 Cov.: 32 AF XY: 0.0252 AC XY: 18337AN XY: 727246
GnomAD4 genome AF: 0.0322 AC: 4908AN: 152218Hom.: 306 Cov.: 32 AF XY: 0.0336 AC XY: 2499AN XY: 74416
ClinVar
Submissions by phenotype
LIPOPROTEIN(a) POLYMORPHISM Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at