rs11119805
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014873.3(LPGAT1):c.*4997A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,680 control chromosomes in the GnomAD database, including 1,354 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.13 ( 1351 hom., cov: 32)
Exomes 𝑓: 0.10 ( 3 hom. )
Consequence
LPGAT1
NM_014873.3 3_prime_UTR
NM_014873.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.23
Genes affected
LPGAT1 (HGNC:28985): (lysophosphatidylglycerol acyltransferase 1) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded protein catalyzes the reacylation of lysophosphatidylglycerol to phosphatidylglycerol, a membrane phospholipid that is an important precursor for the synthesis of cardiolipin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPGAT1 | NM_014873.3 | c.*4997A>T | 3_prime_UTR_variant | 8/8 | ENST00000366997.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPGAT1 | ENST00000366997.9 | c.*4997A>T | 3_prime_UTR_variant | 8/8 | 1 | NM_014873.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.130 AC: 19723AN: 152128Hom.: 1345 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.0995 AC: 43AN: 432Hom.: 3 Cov.: 0 AF XY: 0.108 AC XY: 28AN XY: 260
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GnomAD4 genome ? AF: 0.130 AC: 19766AN: 152248Hom.: 1351 Cov.: 32 AF XY: 0.132 AC XY: 9806AN XY: 74424
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ClinVar
Not reported inComputational 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