20-45902199-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006227.4(PLTP):c.1175+68C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,519,638 control chromosomes in the GnomAD database, including 315,946 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.65 ( 32317 hom., cov: 33)
Exomes 𝑓: 0.64 ( 283629 hom. )
Consequence
PLTP
NM_006227.4 intron
NM_006227.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.618
Publications
15 publications found
Genes affected
PLTP (HGNC:9093): (phospholipid transfer protein) The protein encoded by this gene is one of at least two lipid transfer proteins found in human plasma. The encoded protein transfers phospholipids from triglyceride-rich lipoproteins to high density lipoprotein (HDL). In addition to regulating the size of HDL particles, this protein may be involved in cholesterol metabolism. At least two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLTP | NM_006227.4 | c.1175+68C>A | intron_variant | Intron 12 of 15 | ENST00000372431.8 | NP_006218.1 | ||
PLTP | NM_182676.3 | c.1019+68C>A | intron_variant | Intron 11 of 14 | NP_872617.1 | |||
PLTP | NM_001242921.1 | c.911+68C>A | intron_variant | Intron 10 of 13 | NP_001229850.1 | |||
PLTP | NM_001242920.2 | c.890+68C>A | intron_variant | Intron 10 of 13 | NP_001229849.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.651 AC: 98975AN: 152024Hom.: 32266 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
98975
AN:
152024
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.643 AC: 878830AN: 1367496Hom.: 283629 AF XY: 0.642 AC XY: 438779AN XY: 683216 show subpopulations
GnomAD4 exome
AF:
AC:
878830
AN:
1367496
Hom.:
AF XY:
AC XY:
438779
AN XY:
683216
show subpopulations
African (AFR)
AF:
AC:
20563
AN:
31576
American (AMR)
AF:
AC:
32027
AN:
41462
Ashkenazi Jewish (ASJ)
AF:
AC:
13131
AN:
25220
East Asian (EAS)
AF:
AC:
26879
AN:
38350
South Asian (SAS)
AF:
AC:
55133
AN:
82696
European-Finnish (FIN)
AF:
AC:
35843
AN:
51572
Middle Eastern (MID)
AF:
AC:
2599
AN:
4444
European-Non Finnish (NFE)
AF:
AC:
656354
AN:
1035022
Other (OTH)
AF:
AC:
36301
AN:
57154
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
Heterozygous variant carriers
0
17932
35863
53795
71726
89658
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
17100
34200
51300
68400
85500
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.651 AC: 99086AN: 152142Hom.: 32317 Cov.: 33 AF XY: 0.655 AC XY: 48714AN XY: 74368 show subpopulations
GnomAD4 genome
AF:
AC:
99086
AN:
152142
Hom.:
Cov.:
33
AF XY:
AC XY:
48714
AN XY:
74368
show subpopulations
African (AFR)
AF:
AC:
27033
AN:
41504
American (AMR)
AF:
AC:
11031
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
1853
AN:
3470
East Asian (EAS)
AF:
AC:
3545
AN:
5160
South Asian (SAS)
AF:
AC:
3211
AN:
4826
European-Finnish (FIN)
AF:
AC:
7474
AN:
10576
Middle Eastern (MID)
AF:
AC:
177
AN:
294
European-Non Finnish (NFE)
AF:
AC:
42865
AN:
67988
Other (OTH)
AF:
AC:
1356
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1800
3600
5401
7201
9001
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
808
1616
2424
3232
4040
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2470
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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