rs10455872
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_005577.4(LPA):c.3947+467T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152134 control chromosomes in the gnomAD Genomes database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.043 ( 192 hom., cov: 33)
Consequence
LPA
NM_005577.4 intron
NM_005577.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 6-160589086-A-G is Benign according to our data. Variant chr6-160589086-A-G is described in ClinVar as [Benign]. Clinvar id is 225938. Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPA | NM_005577.4 | c.3947+467T>C | intron_variant | ENST00000316300.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPA | ENST00000316300.10 | c.3947+467T>C | intron_variant | 1 | NM_005577.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0425 AC: 6468AN: 152134Hom.: 192 Cov.: 33
GnomAD3 genomes
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33
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23
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3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
LIPOPROTEIN(a) POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Aug 07, 2020 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at