rs4713951
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001374623.1(PNPLA1):c.715-150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 722,284 control chromosomes in the GnomAD database, including 73,816 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.43 ( 14491 hom., cov: 32)
Exomes 𝑓: 0.45 ( 59325 hom. )
Consequence
PNPLA1
NM_001374623.1 intron
NM_001374623.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.63
Genes affected
PNPLA1 (HGNC:21246): (patatin like phospholipase domain containing 1) The protein encoded by this gene belongs to the patatin-like phospholipase (PNPLA) family, which is characterized by the presence of a highly conserved patatin domain. PNPLA family members have diverse lipolytic and acyltransferase activities, and are key elements in lipid metabolism. While other members of this family have been well characterized, the function of this gene remained an enigma. However, recent studies show that this gene is expressed in the skin epidermal keratinocytes, and has a role in glycerophospholipid metabolism in the cutaneous barrier. Consistent with these observations, mutations in this gene are associated with ichthyosis in human (autosomal recessive congenital ichthyoses, ARCI) and dog. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 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=-0.96).
BP6
?
Variant 6-36295214-C-T is Benign according to our data. Variant chr6-36295214-C-T is described in ClinVar as [Benign]. Clinvar id is 1249564.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPLA1 | NM_001374623.1 | c.715-150C>T | intron_variant | ENST00000636260.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPLA1 | ENST00000636260.2 | c.715-150C>T | intron_variant | 5 | NM_001374623.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.430 AC: 65387AN: 151962Hom.: 14469 Cov.: 32
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GnomAD4 exome AF: 0.447 AC: 254670AN: 570204Hom.: 59325 AF XY: 0.445 AC XY: 133858AN XY: 301034
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GnomAD4 genome ? AF: 0.430 AC: 65445AN: 152080Hom.: 14491 Cov.: 32 AF XY: 0.438 AC XY: 32551AN XY: 74328
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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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at