rs1061808
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006411.4(AGPAT1):c.*506A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 155,158 control chromosomes in the GnomAD database, including 31,887 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 0.64 ( 31367 hom., cov: 31)
Exomes 𝑓: 0.55 ( 520 hom. )
Consequence
AGPAT1
NM_006411.4 3_prime_UTR
NM_006411.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.29
Genes affected
AGPAT1 (HGNC:324): (1-acylglycerol-3-phosphate O-acyltransferase 1) This gene encodes an enzyme that converts lysophosphatidic acid (LPA) into phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. This enzyme localizes to the endoplasmic reticulum. This gene is located in the class III region of the human major histocompatibility complex. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT1 | NM_006411.4 | c.*506A>C | 3_prime_UTR_variant | 7/7 | ENST00000375107.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT1 | ENST00000375107.8 | c.*506A>C | 3_prime_UTR_variant | 7/7 | 1 | NM_006411.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.641 AC: 97273AN: 151750Hom.: 31352 Cov.: 31
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GnomAD4 exome AF: 0.550 AC: 1808AN: 3288Hom.: 520 Cov.: 0 AF XY: 0.560 AC XY: 959AN XY: 1712
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GnomAD4 genome ? AF: 0.641 AC: 97347AN: 151870Hom.: 31367 Cov.: 31 AF XY: 0.640 AC XY: 47489AN XY: 74226
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ClinVar
Not reported inComputational scores
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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