rs7659
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001647.4(APOD):c.*110G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
APOD
NM_001647.4 3_prime_UTR
NM_001647.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00700
Publications
11 publications found
Genes affected
APOD (HGNC:612): (apolipoprotein D) This gene encodes a component of high density lipoprotein that has no marked similarity to other apolipoprotein sequences. It has a high degree of homology to plasma retinol-binding protein and other members of the alpha 2 microglobulin protein superfamily of carrier proteins, also known as lipocalins. This glycoprotein is closely associated with the enzyme lecithin:cholesterol acyltransferase - an enzyme involved in lipoprotein metabolism. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001647.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| APOD | TSL:1 MANE Select | c.*110G>C | 3_prime_UTR | Exon 5 of 5 | ENSP00000345179.3 | P05090 | |||
| APOD | c.*110G>C | 3_prime_UTR | Exon 6 of 6 | ENSP00000623590.1 | |||||
| APOD | c.*110G>C | 3_prime_UTR | Exon 6 of 6 | ENSP00000522585.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 143828Hom.: 0 Cov.: 26
GnomAD3 genomes
AF:
AC:
0
AN:
143828
Hom.:
Cov.:
26
Gnomad AFR
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Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 619172Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 328084
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
619172
Hom.:
Cov.:
8
AF XY:
AC XY:
0
AN XY:
328084
African (AFR)
AF:
AC:
0
AN:
16254
American (AMR)
AF:
AC:
0
AN:
35658
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17128
East Asian (EAS)
AF:
AC:
0
AN:
34466
South Asian (SAS)
AF:
AC:
0
AN:
58000
European-Finnish (FIN)
AF:
AC:
0
AN:
47734
Middle Eastern (MID)
AF:
AC:
0
AN:
2852
European-Non Finnish (NFE)
AF:
AC:
0
AN:
375042
Other (OTH)
AF:
AC:
0
AN:
32038
GnomAD4 genome 0.00 AC: 0AN: 143828Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 70126
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
143828
Hom.:
Cov.:
26
AF XY:
AC XY:
0
AN XY:
70126
African (AFR)
AF:
AC:
0
AN:
35552
American (AMR)
AF:
AC:
0
AN:
14542
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3458
East Asian (EAS)
AF:
AC:
0
AN:
4862
South Asian (SAS)
AF:
AC:
0
AN:
4640
European-Finnish (FIN)
AF:
AC:
0
AN:
10008
Middle Eastern (MID)
AF:
AC:
0
AN:
282
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67614
Other (OTH)
AF:
AC:
0
AN:
1966
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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