rs3812499
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098537.3(PNPLA7):c.2798C>T(p.Pro933Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00435 in 1,347,618 control chromosomes in the GnomAD database, including 370 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 0.0053 ( 51 hom., cov: 33)
Exomes 𝑓: 0.0042 ( 319 hom. )
Consequence
PNPLA7
NM_001098537.3 missense
NM_001098537.3 missense
Scores
2
9
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 9.26
Genes affected
PNPLA7 (HGNC:24768): (patatin like phospholipase domain containing 7) Human patatin-like phospholipases, such as PNPLA7, have been implicated in regulation of adipocyte differentiation and have been induced by metabolic stimuli (Wilson et al., 2006 [PubMed 16799181]).[supplied by OMIM, Jun 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0019916296).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPLA7 | NM_001098537.3 | c.2798C>T | p.Pro933Leu | missense_variant | 25/35 | ENST00000406427.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPLA7 | ENST00000406427.6 | c.2798C>T | p.Pro933Leu | missense_variant | 25/35 | 1 | NM_001098537.3 | P2 | |
PNPLA7 | ENST00000277531.8 | c.2723C>T | p.Pro908Leu | missense_variant | 24/34 | 2 | A2 | ||
PNPLA7 | ENST00000469998.1 | n.1537C>T | non_coding_transcript_exon_variant | 2/10 | 2 | ||||
PNPLA7 | ENST00000492278.5 | n.1314C>T | non_coding_transcript_exon_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00533 AC: 811AN: 152154Hom.: 52 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00739 AC: 253AN: 34230Hom.: 17 AF XY: 0.00742 AC XY: 117AN XY: 15770
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GnomAD4 exome AF: 0.00423 AC: 5051AN: 1195346Hom.: 319 Cov.: 30 AF XY: 0.00409 AC XY: 2357AN XY: 576490
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GnomAD4 genome ? AF: 0.00532 AC: 810AN: 152272Hom.: 51 Cov.: 33 AF XY: 0.00625 AC XY: 465AN XY: 74446
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ExAC
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631
Asia WGS
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180
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
P;D
Vest4
MVP
MPC
0.62
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at