chr16-55525601-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017839.5(LPCAT2):c.265G>A(p.Val89Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00348 in 1,612,162 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 49 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 49 hom. )
Consequence
LPCAT2
NM_017839.5 missense
NM_017839.5 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 2.07
Genes affected
LPCAT2 (HGNC:26032): (lysophosphatidylcholine acyltransferase 2) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002805978).
BP6
?
Variant 16-55525601-G-A is Benign according to our data. Variant chr16-55525601-G-A is described in ClinVar as [Benign]. Clinvar id is 768779.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0145 (2207/152088) while in subpopulation AFR AF= 0.0467 (1936/41496). AF 95% confidence interval is 0.0449. There are 49 homozygotes in gnomad4. There are 1054 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 49 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPCAT2 | NM_017839.5 | c.265G>A | p.Val89Ile | missense_variant | 2/14 | ENST00000262134.10 | |
LPCAT2 | XM_047434277.1 | c.97G>A | p.Val33Ile | missense_variant | 2/14 | ||
LPCAT2 | XM_005256006.4 | c.265G>A | p.Val89Ile | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPCAT2 | ENST00000262134.10 | c.265G>A | p.Val89Ile | missense_variant | 2/14 | 1 | NM_017839.5 | P1 | |
LPCAT2 | ENST00000566911.1 | n.375G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0145 AC: 2206AN: 151970Hom.: 49 Cov.: 32
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GnomAD3 exomes AF: 0.00521 AC: 1303AN: 250032Hom.: 18 AF XY: 0.00422 AC XY: 570AN XY: 135190
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GnomAD4 exome AF: 0.00233 AC: 3408AN: 1460074Hom.: 49 Cov.: 30 AF XY: 0.00211 AC XY: 1535AN XY: 726406
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GnomAD4 genome ? AF: 0.0145 AC: 2207AN: 152088Hom.: 49 Cov.: 32 AF XY: 0.0142 AC XY: 1054AN XY: 74368
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ESP6500AA
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188
ESP6500EA
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ExAC
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691
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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