rs27528
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001040458.3(ERAP1):c.663+40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 1,609,316 control chromosomes in the GnomAD database, including 51,914 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001040458.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERAP1 | ENST00000443439.7 | c.663+40A>G | intron_variant | Intron 3 of 18 | 1 | NM_001040458.3 | ENSP00000406304.2 | |||
ERAP1 | ENST00000296754.7 | c.663+40A>G | intron_variant | Intron 3 of 19 | 1 | ENSP00000296754.3 | ||||
ERAP1 | ENST00000503921.5 | c.-61+2581A>G | intron_variant | Intron 2 of 2 | 4 | ENSP00000427025.1 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38642AN: 152050Hom.: 5051 Cov.: 32
GnomAD3 exomes AF: 0.272 AC: 68198AN: 251024Hom.: 9861 AF XY: 0.268 AC XY: 36366AN XY: 135724
GnomAD4 exome AF: 0.251 AC: 365656AN: 1457148Hom.: 46856 Cov.: 30 AF XY: 0.252 AC XY: 182499AN XY: 725208
GnomAD4 genome AF: 0.254 AC: 38675AN: 152168Hom.: 5058 Cov.: 32 AF XY: 0.258 AC XY: 19181AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 45. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at