rs3131300
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136.5(AGER):c.52+14T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,609,916 control chromosomes in the GnomAD database, including 25,894 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 0.14 ( 1733 hom., cov: 32)
Exomes 𝑓: 0.18 ( 24161 hom. )
Consequence
AGER
NM_001136.5 intron
NM_001136.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.826
Genes affected
AGER (HGNC:320): (advanced glycosylation end-product specific receptor) The advanced glycosylation end product (AGE) receptor encoded by this gene is a member of the immunoglobulin superfamily of cell surface receptors. It is a multiligand receptor, and besides AGE, interacts with other molecules implicated in homeostasis, development, and inflammation, and certain diseases, such as diabetes and Alzheimer's disease. Many alternatively spliced transcript variants encoding different isoforms, as well as non-protein-coding variants, have been described for this gene (PMID:18089847). [provided by RefSeq, May 2011]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGER | NM_001136.5 | c.52+14T>C | intron_variant | ENST00000375076.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGER | ENST00000375076.9 | c.52+14T>C | intron_variant | 1 | NM_001136.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21837AN: 151970Hom.: 1738 Cov.: 32
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GnomAD3 exomes AF: 0.135 AC: 32805AN: 242884Hom.: 2519 AF XY: 0.137 AC XY: 18160AN XY: 132340
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GnomAD4 exome AF: 0.175 AC: 255563AN: 1457828Hom.: 24161 Cov.: 56 AF XY: 0.173 AC XY: 125573AN XY: 725120
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GnomAD4 genome ? AF: 0.144 AC: 21827AN: 152088Hom.: 1733 Cov.: 32 AF XY: 0.139 AC XY: 10339AN XY: 74344
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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