chr21-14144714-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001302998.2(LIPI):āc.1204T>Cā(p.Leu402=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000617 in 1,572,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.000072 ( 0 hom., cov: 32)
Exomes š: 0.000061 ( 0 hom. )
Consequence
LIPI
NM_001302998.2 synonymous
NM_001302998.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.615
Genes affected
LIPI (HGNC:18821): (lipase I) The protein encoded by this gene is a phospholipase that hydrolyzes phosphatidic acid to produce lysophosphatidic acid. Defects in this gene are a cause of susceptibility to familial hypertrigliceridemia. This gene is also expressed at high levels in Ewing family tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 21-14144714-A-G is Benign according to our data. Variant chr21-14144714-A-G is described in ClinVar as [Benign]. Clinvar id is 2182800.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.615 with no splicing effect.
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPI | NM_001302998.2 | c.1204T>C | p.Leu402= | synonymous_variant | 9/10 | ENST00000681601.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPI | ENST00000681601.1 | c.1204T>C | p.Leu402= | synonymous_variant | 9/10 | NM_001302998.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000958 AC: 24AN: 250596Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135456
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GnomAD4 exome AF: 0.0000606 AC: 86AN: 1419868Hom.: 0 Cov.: 26 AF XY: 0.0000719 AC XY: 51AN XY: 709132
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74326
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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 | Invitae | Sep 19, 2022 | - - |
Computational scores
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Benign
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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