rs9267528
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000375920.8(APOM):c.-103+1813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00582 in 152,194 control chromosomes in the GnomAD database, including 8 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 0.0058 ( 8 hom., cov: 32)
Consequence
APOM
ENST00000375920.8 intron
ENST00000375920.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.151
Genes affected
APOM (HGNC:13916): (apolipoprotein M) The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012]
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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=-0.72).
BS2
?
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOM | NM_001256169.2 | c.-103+1813C>T | intron_variant | ||||
APOM | NR_045828.2 | n.148+1813C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOM | ENST00000375920.8 | c.-103+1813C>T | intron_variant | 1 | |||||
APOM | ENST00000375918.6 | c.-103+1813C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00582 AC: 885AN: 152076Hom.: 8 Cov.: 32
GnomAD3 genomes
?
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885
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152076
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00582 AC: 886AN: 152194Hom.: 8 Cov.: 32 AF XY: 0.00586 AC XY: 436AN XY: 74424
GnomAD4 genome
?
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AC:
886
AN:
152194
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32
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436
AN XY:
74424
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16
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at