chr2-198184384-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000625084.1(PLCL1):n.44+34966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,154 control chromosomes in the GnomAD database, including 10,674 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 0.36 ( 10674 hom., cov: 33)
Consequence
PLCL1
ENST00000625084.1 intron
ENST00000625084.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.166
Publications
1 publications found
Genes affected
PLCL1 (HGNC:9063): (phospholipase C like 1 (inactive)) Predicted to enable phospholipase C activity. Predicted to be involved in negative regulation of cold-induced thermogenesis and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within several processes, including gamma-aminobutyric acid signaling pathway; regulation of GABAergic synaptic transmission; and regulation of peptidyl-serine phosphorylation. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCL1 | ENST00000625084.1 | n.44+34966A>G | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.361 AC: 54866AN: 152036Hom.: 10680 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
54866
AN:
152036
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.361 AC: 54867AN: 152154Hom.: 10674 Cov.: 33 AF XY: 0.358 AC XY: 26661AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
54867
AN:
152154
Hom.:
Cov.:
33
AF XY:
AC XY:
26661
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
8485
AN:
41534
American (AMR)
AF:
AC:
5259
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
1927
AN:
3468
East Asian (EAS)
AF:
AC:
2331
AN:
5178
South Asian (SAS)
AF:
AC:
1669
AN:
4824
European-Finnish (FIN)
AF:
AC:
4224
AN:
10568
Middle Eastern (MID)
AF:
AC:
174
AN:
294
European-Non Finnish (NFE)
AF:
AC:
29575
AN:
67974
Other (OTH)
AF:
AC:
861
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1768
3535
5303
7070
8838
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
542
1084
1626
2168
2710
<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:
1269
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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