rs61929725
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001128203.2(PLAAT3):c.15+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,512,162 control chromosomes in the GnomAD database, including 13,822 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 0.11 ( 1051 hom., cov: 32)
Exomes 𝑓: 0.13 ( 12771 hom. )
Consequence
PLAAT3
NM_001128203.2 intron
NM_001128203.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.40
Publications
4 publications found
Genes affected
PLAAT3 (HGNC:17825): (phospholipase A and acyltransferase 3) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma. [provided by Alliance of Genome Resources, Apr 2022]
PLAAT3 Gene-Disease associations (from GenCC):
- lipodystrophy, familial partial, type 9Inheritance: AR Classification: LIMITED Submitted by: G2P, Ambry Genetics
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=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLAAT3 | NM_001128203.2 | c.15+14G>A | intron_variant | Intron 2 of 4 | ENST00000415826.3 | NP_001121675.1 | ||
PLAAT3 | NM_007069.3 | c.15+14G>A | intron_variant | Intron 1 of 3 | NP_009000.2 | |||
PLAAT3 | XM_011544741.2 | c.60+2601G>A | intron_variant | Intron 1 of 3 | XP_011543043.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLAAT3 | ENST00000415826.3 | c.15+14G>A | intron_variant | Intron 2 of 4 | 2 | NM_001128203.2 | ENSP00000389124.1 | |||
PLAAT3 | ENST00000323646.9 | c.15+14G>A | intron_variant | Intron 1 of 3 | 1 | ENSP00000320337.5 | ||||
PLAAT3 | ENST00000394613.3 | n.159+14G>A | intron_variant | Intron 1 of 3 | 1 | |||||
PLAAT3 | ENST00000544269.1 | n.297+2601G>A | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.109 AC: 16629AN: 152182Hom.: 1053 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
16629
AN:
152182
Hom.:
Cov.:
32
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:
GnomAD2 exomes AF: 0.113 AC: 27899AN: 247108 AF XY: 0.117 show subpopulations
GnomAD2 exomes
AF:
AC:
27899
AN:
247108
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.128 AC: 173912AN: 1359862Hom.: 12771 Cov.: 22 AF XY: 0.129 AC XY: 88047AN XY: 681578 show subpopulations
GnomAD4 exome
AF:
AC:
173912
AN:
1359862
Hom.:
Cov.:
22
AF XY:
AC XY:
88047
AN XY:
681578
show subpopulations
African (AFR)
AF:
AC:
2032
AN:
31570
American (AMR)
AF:
AC:
3165
AN:
44440
Ashkenazi Jewish (ASJ)
AF:
AC:
4400
AN:
25450
East Asian (EAS)
AF:
AC:
86
AN:
39196
South Asian (SAS)
AF:
AC:
10789
AN:
84100
European-Finnish (FIN)
AF:
AC:
4560
AN:
53268
Middle Eastern (MID)
AF:
AC:
973
AN:
5546
European-Non Finnish (NFE)
AF:
AC:
140566
AN:
1019160
Other (OTH)
AF:
AC:
7341
AN:
57132
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
7466
14932
22397
29863
37329
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4662
9324
13986
18648
23310
<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: 0.109 AC: 16622AN: 152300Hom.: 1051 Cov.: 32 AF XY: 0.106 AC XY: 7906AN XY: 74472 show subpopulations
GnomAD4 genome
AF:
AC:
16622
AN:
152300
Hom.:
Cov.:
32
AF XY:
AC XY:
7906
AN XY:
74472
show subpopulations
African (AFR)
AF:
AC:
2688
AN:
41578
American (AMR)
AF:
AC:
1544
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
610
AN:
3470
East Asian (EAS)
AF:
AC:
28
AN:
5178
South Asian (SAS)
AF:
AC:
648
AN:
4826
European-Finnish (FIN)
AF:
AC:
836
AN:
10612
Middle Eastern (MID)
AF:
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
AC:
9797
AN:
68008
Other (OTH)
AF:
AC:
291
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
791
1582
2372
3163
3954
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
192
384
576
768
960
<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:
264
AN:
3478
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.