chr15-89677777-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002666.5(PLIN1):c.-14-274A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 425,028 control chromosomes in the GnomAD database, including 162,939 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.88 ( 58101 hom., cov: 21)
Exomes 𝑓: 0.85 ( 104838 hom. )
Consequence
PLIN1
NM_002666.5 intron
NM_002666.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.679
Genes affected
PLIN1 (HGNC:9076): (perilipin 1) The protein encoded by this gene coats lipid storage droplets in adipocytes, thereby protecting them until they can be broken down by hormone-sensitive lipase. The encoded protein is the major cAMP-dependent protein kinase substrate in adipocytes and, when unphosphorylated, may play a role in the inhibition of lipolysis. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Feb 2009]
PEX11A (HGNC:8852): (peroxisomal biogenesis factor 11 alpha) This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
?
Variant 15-89677777-T-G is Benign according to our data. Variant chr15-89677777-T-G is described in ClinVar as [Benign]. Clinvar id is 1178857.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.-14-274A>C | intron_variant | ENST00000300055.10 | |||
PLIN1 | NM_001145311.2 | c.-14-274A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.-14-274A>C | intron_variant | 1 | NM_002666.5 | P1 | |||
PLIN1 | ENST00000531697.1 | n.97-274A>C | intron_variant, non_coding_transcript_variant | 1 | |||||
PLIN1 | ENST00000430628.2 | c.-14-274A>C | intron_variant | 5 | P1 | ||||
PEX11A | ENST00000557982.1 | n.633A>C | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.879 AC: 128968AN: 146692Hom.: 58067 Cov.: 21
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GnomAD4 exome AF: 0.850 AC: 236413AN: 278258Hom.: 104838 Cov.: 0 AF XY: 0.844 AC XY: 123527AN XY: 146304
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GnomAD4 genome ? AF: 0.879 AC: 129035AN: 146770Hom.: 58101 Cov.: 21 AF XY: 0.866 AC XY: 61774AN XY: 71310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at