NM_020376.4:c.696+91G>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS1
The NM_020376.4(PNPLA2):c.696+91G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,128,920 control chromosomes in the GnomAD database, including 1 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 0.00054 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 1 hom. )
Consequence
PNPLA2
NM_020376.4 intron
NM_020376.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.138
Publications
1 publications found
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 myopathyInheritance: 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: Likely_benign. The variant received -4 ACMG points.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000538 (82/152368) while in subpopulation AFR AF = 0.00192 (80/41586). AF 95% confidence interval is 0.00158. There are 0 homozygotes in GnomAd4. There are 31 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNPLA2 | ENST00000336615.9 | c.696+91G>C | intron_variant | Intron 5 of 9 | 1 | NM_020376.4 | ENSP00000337701.4 | |||
PNPLA2 | ENST00000525250.5 | n.1302+91G>C | intron_variant | Intron 3 of 5 | 2 | |||||
PNPLA2 | ENST00000531923.1 | n.591+91G>C | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000532 AC: 81AN: 152250Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
81
AN:
152250
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:
GnomAD4 exome AF: 0.000102 AC: 100AN: 976552Hom.: 1 AF XY: 0.0000793 AC XY: 40AN XY: 504530 show subpopulations
GnomAD4 exome
AF:
AC:
100
AN:
976552
Hom.:
AF XY:
AC XY:
40
AN XY:
504530
show subpopulations
African (AFR)
AF:
AC:
77
AN:
24102
American (AMR)
AF:
AC:
11
AN:
43220
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23044
East Asian (EAS)
AF:
AC:
0
AN:
36892
South Asian (SAS)
AF:
AC:
2
AN:
76082
European-Finnish (FIN)
AF:
AC:
0
AN:
40020
Middle Eastern (MID)
AF:
AC:
0
AN:
3638
European-Non Finnish (NFE)
AF:
AC:
0
AN:
685074
Other (OTH)
AF:
AC:
10
AN:
44480
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
6
11
17
22
28
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4
8
12
16
20
<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: 0.000538 AC: 82AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74506 show subpopulations
GnomAD4 genome
AF:
AC:
82
AN:
152368
Hom.:
Cov.:
33
AF XY:
AC XY:
31
AN XY:
74506
show subpopulations
African (AFR)
AF:
AC:
80
AN:
41586
American (AMR)
AF:
AC:
2
AN:
15314
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68032
Other (OTH)
AF:
AC:
0
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.490
Heterozygous variant carriers
0
4
8
11
15
19
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<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:
4
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
DS_DG_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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