rs3753526
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_003101.6(SOAT1):āc.1425C>Gā(p.Leu475=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 1,612,522 control chromosomes in the GnomAD database, including 11,203 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: š 0.099 ( 1083 hom., cov: 33)
Exomes š: 0.096 ( 10120 hom. )
Consequence
SOAT1
NM_003101.6 synonymous
NM_003101.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.241
Genes affected
SOAT1 (HGNC:11177): (sterol O-acyltransferase 1) The protein encoded by this gene belongs to the acyltransferase family. It is located in the endoplasmic reticulum, and catalyzes the formation of fatty acid-cholesterol esters. This gene has been implicated in the formation of beta-amyloid and atherosclerotic plaques by controlling the equilibrium between free cholesterol and cytoplasmic cholesteryl esters. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]
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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=-0.34).
BP7
?
Synonymous conserved (PhyloP=0.241 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOAT1 | NM_003101.6 | c.1425C>G | p.Leu475= | synonymous_variant | 14/16 | ENST00000367619.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOAT1 | ENST00000367619.8 | c.1425C>G | p.Leu475= | synonymous_variant | 14/16 | 1 | NM_003101.6 | P1 | |
SOAT1 | ENST00000540564.5 | c.1251C>G | p.Leu417= | synonymous_variant | 13/15 | 1 | |||
SOAT1 | ENST00000539888.5 | c.1230C>G | p.Leu410= | synonymous_variant | 13/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0992 AC: 15083AN: 151992Hom.: 1084 Cov.: 33
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GnomAD3 exomes AF: 0.134 AC: 33580AN: 251326Hom.: 3447 AF XY: 0.129 AC XY: 17459AN XY: 135844
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GnomAD4 exome AF: 0.0964 AC: 140815AN: 1460412Hom.: 10120 Cov.: 32 AF XY: 0.0973 AC XY: 70712AN XY: 726598
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GnomAD4 genome ? AF: 0.0992 AC: 15088AN: 152110Hom.: 1083 Cov.: 33 AF XY: 0.105 AC XY: 7832AN XY: 74342
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at