5-96788627-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001040458.3(ERAP1):c.1583A>G(p.Lys528Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,613,788 control chromosomes in the GnomAD database, including 336,155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001040458.3 missense
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.1583A>G | p.Lys528Arg | missense_variant | Exon 11 of 19 | 1 | NM_001040458.3 | ENSP00000406304.2 | ||
ERAP1 | ENST00000296754.7 | c.1583A>G | p.Lys528Arg | missense_variant | Exon 11 of 20 | 1 | ENSP00000296754.3 | |||
ERAP1 | ENST00000507859.1 | n.246A>G | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.624 AC: 94853AN: 151930Hom.: 29810 Cov.: 32
GnomAD3 exomes AF: 0.620 AC: 155788AN: 251240Hom.: 48690 AF XY: 0.621 AC XY: 84267AN XY: 135782
GnomAD4 exome AF: 0.646 AC: 943908AN: 1461740Hom.: 306314 Cov.: 55 AF XY: 0.644 AC XY: 468530AN XY: 727174
GnomAD4 genome AF: 0.624 AC: 94930AN: 152048Hom.: 29841 Cov.: 32 AF XY: 0.621 AC XY: 46193AN XY: 74328
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 78% of patients studied by a panel of primary immunodeficiencies. Number of patients: 69. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at