rs61929725

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Publications

4 publications found
Variant links:
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 9
    Inheritance: 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
PLAAT3NM_001128203.2 linkc.15+14G>A intron_variant Intron 2 of 4 ENST00000415826.3 NP_001121675.1 P53816A0A024R561
PLAAT3NM_007069.3 linkc.15+14G>A intron_variant Intron 1 of 3 NP_009000.2 P53816A0A024R561
PLAAT3XM_011544741.2 linkc.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
PLAAT3ENST00000415826.3 linkc.15+14G>A intron_variant Intron 2 of 4 2 NM_001128203.2 ENSP00000389124.1 P53816
PLAAT3ENST00000323646.9 linkc.15+14G>A intron_variant Intron 1 of 3 1 ENSP00000320337.5 P53816
PLAAT3ENST00000394613.3 linkn.159+14G>A intron_variant Intron 1 of 3 1
PLAAT3ENST00000544269.1 linkn.297+2601G>A intron_variant Intron 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16629
AN:
152182
Hom.:
1053
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0648
Gnomad AMI
AF:
0.136
Gnomad AMR
AF:
0.101
Gnomad ASJ
AF:
0.176
Gnomad EAS
AF:
0.00539
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.0788
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.138
GnomAD2 exomes
AF:
0.113
AC:
27899
AN:
247108
AF XY:
0.117
show subpopulations
Gnomad AFR exome
AF:
0.0668
Gnomad AMR exome
AF:
0.0670
Gnomad ASJ exome
AF:
0.173
Gnomad EAS exome
AF:
0.00425
Gnomad FIN exome
AF:
0.0812
Gnomad NFE exome
AF:
0.146
Gnomad OTH exome
AF:
0.142
GnomAD4 exome
AF:
0.128
AC:
173912
AN:
1359862
Hom.:
12771
Cov.:
22
AF XY:
0.129
AC XY:
88047
AN XY:
681578
show subpopulations
African (AFR)
AF:
0.0644
AC:
2032
AN:
31570
American (AMR)
AF:
0.0712
AC:
3165
AN:
44440
Ashkenazi Jewish (ASJ)
AF:
0.173
AC:
4400
AN:
25450
East Asian (EAS)
AF:
0.00219
AC:
86
AN:
39196
South Asian (SAS)
AF:
0.128
AC:
10789
AN:
84100
European-Finnish (FIN)
AF:
0.0856
AC:
4560
AN:
53268
Middle Eastern (MID)
AF:
0.175
AC:
973
AN:
5546
European-Non Finnish (NFE)
AF:
0.138
AC:
140566
AN:
1019160
Other (OTH)
AF:
0.128
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:
16622
AN:
152300
Hom.:
1051
Cov.:
32
AF XY:
0.106
AC XY:
7906
AN XY:
74472
show subpopulations
African (AFR)
AF:
0.0646
AC:
2688
AN:
41578
American (AMR)
AF:
0.101
AC:
1544
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
0.176
AC:
610
AN:
3470
East Asian (EAS)
AF:
0.00541
AC:
28
AN:
5178
South Asian (SAS)
AF:
0.134
AC:
648
AN:
4826
European-Finnish (FIN)
AF:
0.0788
AC:
836
AN:
10612
Middle Eastern (MID)
AF:
0.190
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
0.144
AC:
9797
AN:
68008
Other (OTH)
AF:
0.138
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:
0.132
Hom.:
410
Bravo
AF:
0.109
Asia WGS
AF:
0.0760
AC:
264
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
2.1
DANN
Benign
0.92
PhyloP100
-2.4
PromoterAI
-0.025
Neutral
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs61929725; hg19: chr11-63381458; API