rs8102428
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367868.2(PLIN4):c.197-292T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,144 control chromosomes in the GnomAD database, including 6,156 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 0.21 ( 6156 hom., cov: 33)
Consequence
PLIN4
NM_001367868.2 intron
NM_001367868.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.29
Genes affected
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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 (BayesDel_noAF=-1.01).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN4 | NM_001367868.2 | c.197-292T>C | intron_variant | ENST00000301286.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN4 | ENST00000301286.5 | c.197-292T>C | intron_variant | 5 | NM_001367868.2 | P1 | |||
PLIN4 | ENST00000633942.1 | c.197-292T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31398AN: 152026Hom.: 6133 Cov.: 33
GnomAD3 genomes
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152026
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.207 AC: 31474AN: 152144Hom.: 6156 Cov.: 33 AF XY: 0.198 AC XY: 14750AN XY: 74400
GnomAD4 genome
?
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AC:
31474
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152144
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33
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14750
AN XY:
74400
Gnomad4 AFR
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Asia WGS
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201
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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