3-195571307-G-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001647.4(APOD):āc.304C>Gā(p.Pro102Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00028 in 1,614,100 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00026 ( 0 hom., cov: 32)
Exomes š: 0.00028 ( 3 hom. )
Consequence
APOD
NM_001647.4 missense
NM_001647.4 missense
Scores
2
1
16
Clinical Significance
Conservation
PhyloP100: 4.40
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 made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.01632744).
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOD | NM_001647.4 | c.304C>G | p.Pro102Ala | missense_variant | 4/5 | ENST00000343267.8 | NP_001638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOD | ENST00000343267.8 | c.304C>G | p.Pro102Ala | missense_variant | 4/5 | 1 | NM_001647.4 | ENSP00000345179.3 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152114Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000505 AC: 127AN: 251488Hom.: 0 AF XY: 0.000581 AC XY: 79AN XY: 135918
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GnomAD4 exome AF: 0.000282 AC: 412AN: 1461868Hom.: 3 Cov.: 31 AF XY: 0.000344 AC XY: 250AN XY: 727236
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GnomAD4 genome AF: 0.000263 AC: 40AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74438
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.304C>G (p.P102A) alteration is located in exon 4 (coding exon 3) of the APOD gene. This alteration results from a C to G substitution at nucleotide position 304, causing the proline (P) at amino acid position 102 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D
REVEL
Benign
Sift
Benign
T;T;D
Sift4G
Benign
T;.;.
Polyphen
B;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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