rs3796677
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001134.3(AFP):c.85+87A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AFP
NM_001134.3 intron
NM_001134.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.690
Publications
5 publications found
Genes affected
AFP (HGNC:317): (alpha fetoprotein) This gene encodes alpha-fetoprotein, a major plasma protein produced by the yolk sac and the liver during fetal life. Alpha-fetoprotein expression in adults is often associated with hepatocarcinoma and with teratoma, and has prognostic value for managing advanced gastric cancer. However, hereditary persistance of alpha-fetoprotein may also be found in individuals with no obvious pathology. The protein is thought to be the fetal counterpart of serum albumin, and the alpha-fetoprotein and albumin genes are present in tandem in the same transcriptional orientation on chromosome 4. Alpha-fetoprotein is found in monomeric as well as dimeric and trimeric forms, and binds copper, nickel, fatty acids and bilirubin. The level of alpha-fetoprotein in amniotic fluid is used to measure renal loss of protein to screen for spina bifida and anencephaly. [provided by RefSeq, Oct 2019]
AFP Gene-Disease associations (from GenCC):
- hereditary persistence of alpha-fetoproteinInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- congenital deficiency in alpha-fetoproteinInheritance: AR Classification: NO_KNOWN Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| AFP | ENST00000395792.7 | c.85+87A>C | intron_variant | Intron 1 of 14 | 1 | NM_001134.3 | ENSP00000379138.2 | |||
| AFP | ENST00000513720.5 | n.147-726A>C | intron_variant | Intron 1 of 1 | 1 | |||||
| AFP | ENST00000515675.1 | n.267-726A>C | intron_variant | Intron 2 of 2 | 1 | |||||
| AFP | ENST00000226359.2 | c.85+87A>C | intron_variant | Intron 1 of 13 | 5 | ENSP00000226359.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 608058Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 321652
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
608058
Hom.:
AF XY:
AC XY:
0
AN XY:
321652
African (AFR)
AF:
AC:
0
AN:
14468
American (AMR)
AF:
AC:
0
AN:
18922
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16880
East Asian (EAS)
AF:
AC:
0
AN:
30390
South Asian (SAS)
AF:
AC:
0
AN:
48860
European-Finnish (FIN)
AF:
AC:
0
AN:
43042
Middle Eastern (MID)
AF:
AC:
0
AN:
2250
European-Non Finnish (NFE)
AF:
AC:
0
AN:
403040
Other (OTH)
AF:
AC:
0
AN:
30206
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
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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