chr15-40303426-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004573.3(PLCB2):c.163-70C>T 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 1,113,060 control chromosomes in the GnomAD database, including 232,056 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 0.60 ( 27953 hom., cov: 30)
Exomes 𝑓: 0.65 ( 204103 hom. )
Consequence
PLCB2
NM_004573.3 intron
NM_004573.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.181
Publications
30 publications found
Genes affected
PLCB2 (HGNC:9055): (phospholipase C beta 2) The protein encoded by this gene is a phosphodiesterase that catalyzes the hydrolysis of phosphatidylinositol 4,5-bisphosphate to the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol. The encoded protein is activated by G proteins and has been shown to be involved in the type 2 taste receptor signal transduction pathway. In addition, nuclear factor kappa B can regulate the transcription of this gene, whose protein product is also an important regulator of platelet responses. [provided by RefSeq, Jan 2017]
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLCB2 | NM_004573.3 | c.163-70C>T | intron_variant | Intron 2 of 31 | ENST00000260402.8 | NP_004564.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.602 AC: 91318AN: 151698Hom.: 27925 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
91318
AN:
151698
Hom.:
Cov.:
30
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: 0.650 AC: 625050AN: 961244Hom.: 204103 AF XY: 0.649 AC XY: 323725AN XY: 499020 show subpopulations
GnomAD4 exome
AF:
AC:
625050
AN:
961244
Hom.:
AF XY:
AC XY:
323725
AN XY:
499020
show subpopulations
African (AFR)
AF:
AC:
12959
AN:
24000
American (AMR)
AF:
AC:
32681
AN:
42450
Ashkenazi Jewish (ASJ)
AF:
AC:
14472
AN:
22656
East Asian (EAS)
AF:
AC:
31510
AN:
37462
South Asian (SAS)
AF:
AC:
51458
AN:
75582
European-Finnish (FIN)
AF:
AC:
34907
AN:
51562
Middle Eastern (MID)
AF:
AC:
3204
AN:
4838
European-Non Finnish (NFE)
AF:
AC:
415824
AN:
658742
Other (OTH)
AF:
AC:
28035
AN:
43952
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.530
Heterozygous variant carriers
0
10896
21793
32689
43586
54482
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
8672
17344
26016
34688
43360
<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: 0.602 AC: 91397AN: 151816Hom.: 27953 Cov.: 30 AF XY: 0.610 AC XY: 45257AN XY: 74182 show subpopulations
GnomAD4 genome
AF:
AC:
91397
AN:
151816
Hom.:
Cov.:
30
AF XY:
AC XY:
45257
AN XY:
74182
show subpopulations
African (AFR)
AF:
AC:
21862
AN:
41356
American (AMR)
AF:
AC:
10328
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
2194
AN:
3464
East Asian (EAS)
AF:
AC:
4116
AN:
5152
South Asian (SAS)
AF:
AC:
3234
AN:
4802
European-Finnish (FIN)
AF:
AC:
7057
AN:
10574
Middle Eastern (MID)
AF:
AC:
173
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40700
AN:
67880
Other (OTH)
AF:
AC:
1260
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1813
3626
5438
7251
9064
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
774
1548
2322
3096
3870
<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:
2517
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.