chr21-14163413-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001302998.2(LIPI):c.1006+6T>A variant causes a splice donor region, intron change. The variant allele was found at a frequency of 0.000285 in 1,277,214 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 (★).
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
LIPI
NM_001302998.2 splice_donor_region, intron
NM_001302998.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.9331
2
Clinical Significance
Conservation
PhyloP100: 5.25
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 21-14163413-A-T is Benign according to our data. Variant chr21-14163413-A-T is described in ClinVar as [Benign]. Clinvar id is 2071599.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 242 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPI | NM_001302998.2 | c.1006+6T>A | splice_donor_region_variant, intron_variant | ENST00000681601.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPI | ENST00000681601.1 | c.1006+6T>A | splice_donor_region_variant, intron_variant | NM_001302998.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00159 AC: 242AN: 152010Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000353 AC: 88AN: 249460Hom.: 0 AF XY: 0.000230 AC XY: 31AN XY: 134830
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GnomAD4 exome AF: 0.000108 AC: 122AN: 1125086Hom.: 0 Cov.: 16 AF XY: 0.0000903 AC XY: 52AN XY: 575900
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GnomAD4 genome ? AF: 0.00159 AC: 242AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 117AN XY: 74374
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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 | Jun 29, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 6
Find out detailed SpliceAI scores and Pangolin per-transcript scores at