rs402781
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000404459.2(LIPN):c.535+244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,784 control chromosomes in the GnomAD database, including 2,852 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 2852 hom., cov: 31)
Consequence
LIPN
ENST00000404459.2 intron
ENST00000404459.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.262
Genes affected
LIPN (HGNC:23452): (lipase family member N) The gene encodes a lipase that is highly expressed in granular keratinocytes in the epidermis, and plays a role in the differentiation of keratinocytes. Mutations in this gene are associated with lamellar ichthyosis type 4. [provided by RefSeq, Dec 2011]
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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=-0.9).
BP6
Variant 10-88766622-C-T is Benign according to our data. Variant chr10-88766622-C-T is described in ClinVar as [Benign]. Clinvar id is 1282002.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPN | NM_001102469.2 | c.535+244C>T | intron_variant | ENST00000404459.2 | NP_001095939.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPN | ENST00000404459.2 | c.535+244C>T | intron_variant | 1 | NM_001102469.2 | ENSP00000383923 | P1 | |||
LIPN | ENST00000674982.1 | n.2572C>T | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes AF: 0.193 AC: 29347AN: 151666Hom.: 2843 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.194 AC: 29384AN: 151784Hom.: 2852 Cov.: 31 AF XY: 0.191 AC XY: 14166AN XY: 74176
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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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Name
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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