GeneBe

11-822820-C-CTCT

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_020376.4(PNPLA2):​c.696+215_696+216insCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 12903 hom., cov: 0)

Consequence

PNPLA2
NM_020376.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77

Publications

2 publications found
Variant links:
Genes affected
PNPLA2 (HGNC:30802): (patatin like phospholipase domain containing 2) This gene encodes an enzyme which catalyzes the first step in the hydrolysis of triglycerides in adipose tissue. Mutations in this gene are associated with neutral lipid storage disease with myopathy. [provided by RefSeq, Jul 2010]
PNPLA2 Gene-Disease associations (from GenCC):
  • neutral lipid storage myopathy
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, G2P, Labcorp Genetics (formerly Invitae), Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PNPLA2NM_020376.4 linkc.696+215_696+216insCTT intron_variant Intron 5 of 9 ENST00000336615.9 NP_065109.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PNPLA2ENST00000336615.9 linkc.696+214_696+215insTCT intron_variant Intron 5 of 9 1 NM_020376.4 ENSP00000337701.4
PNPLA2ENST00000525250.5 linkn.1302+214_1302+215insTCT intron_variant Intron 3 of 5 2
PNPLA2ENST00000531923.1 linkn.591+214_591+215insTCT intron_variant Intron 1 of 1 2
ENSG00000255108ENST00000532946.2 linkn.*214_*215insAGA downstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.394
AC:
51935
AN:
131654
Hom.:
12903
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.624
Gnomad AMR
AF:
0.528
Gnomad ASJ
AF:
0.410
Gnomad EAS
AF:
0.236
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.489
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.394
AC:
51922
AN:
131628
Hom.:
12903
Cov.:
0
AF XY:
0.383
AC XY:
23821
AN XY:
62172
show subpopulations
African (AFR)
AF:
0.121
AC:
4422
AN:
36410
American (AMR)
AF:
0.528
AC:
6651
AN:
12596
Ashkenazi Jewish (ASJ)
AF:
0.410
AC:
1348
AN:
3284
East Asian (EAS)
AF:
0.236
AC:
1097
AN:
4656
South Asian (SAS)
AF:
0.200
AC:
854
AN:
4278
European-Finnish (FIN)
AF:
0.489
AC:
2425
AN:
4962
Middle Eastern (MID)
AF:
0.378
AC:
90
AN:
238
European-Non Finnish (NFE)
AF:
0.540
AC:
33771
AN:
62582
Other (OTH)
AF:
0.414
AC:
732
AN:
1770
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1116
2232
3349
4465
5581
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
464
928
1392
1856
2320
<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:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs10544581; hg19: chr11-822820; COSMIC: COSV60744406; COSMIC: COSV60744406; API