rs149078
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040458.3(ERAP1):c.2670+934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,994 control chromosomes in the GnomAD database, including 8,882 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 0.33 ( 8882 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
ERAP1
NM_001040458.3 intron
NM_001040458.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.209
Genes affected
ERAP1 (HGNC:18173): (endoplasmic reticulum aminopeptidase 1) The protein encoded by this gene is an aminopeptidase involved in trimming HLA class I-binding precursors so that they can be presented on MHC class I molecules. The encoded protein acts as a monomer or as a heterodimer with ERAP2. This protein may also be involved in blood pressure regulation by inactivation of angiotensin II. Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Oct 2010]
CAST (HGNC:1515): (calpastatin) The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1-4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERAP1 | NM_001040458.3 | c.2670+934C>T | intron_variant | ENST00000443439.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERAP1 | ENST00000443439.7 | c.2670+934C>T | intron_variant | 1 | NM_001040458.3 | P1 | |||
ERAP1 | ENST00000296754.7 | c.2670+934C>T | intron_variant | 1 | |||||
CAST | ENST00000510098.1 | c.*605G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 1 | ||||
ERAP1 | ENST00000512852.1 | c.206+934C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.334 AC: 50768AN: 151872Hom.: 8867 Cov.: 32
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.334 AC: 50830AN: 151992Hom.: 8882 Cov.: 32 AF XY: 0.334 AC XY: 24797AN XY: 74302
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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