rs3796676
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134.3(AFP):c.85+151T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 550,668 control chromosomes in the GnomAD database, including 58,564 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 0.46 ( 16605 hom., cov: 32)
Exomes 𝑓: 0.45 ( 41959 hom. )
Consequence
AFP
NM_001134.3 intron
NM_001134.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.176
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFP | NM_001134.3 | c.85+151T>A | intron_variant | ENST00000395792.7 | |||
AFP | NM_001354717.2 | c.-248+151T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFP | ENST00000395792.7 | c.85+151T>A | intron_variant | 1 | NM_001134.3 | P1 | |||
AFP | ENST00000513720.5 | n.147-662T>A | intron_variant, non_coding_transcript_variant | 1 | |||||
AFP | ENST00000515675.1 | n.267-662T>A | intron_variant, non_coding_transcript_variant | 1 | |||||
AFP | ENST00000226359.2 | c.85+151T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.464 AC: 70197AN: 151424Hom.: 16574 Cov.: 32
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GnomAD4 exome AF: 0.452 AC: 180465AN: 399126Hom.: 41959 AF XY: 0.451 AC XY: 96007AN XY: 212776
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GnomAD4 genome ? AF: 0.464 AC: 70290AN: 151542Hom.: 16605 Cov.: 32 AF XY: 0.468 AC XY: 34655AN XY: 74060
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ClinVar
Not reported inComputational scores
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Name
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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