5-96803761-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040458.3(ERAP1):c.166G>A(p.Glu56Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 1,614,084 control chromosomes in the GnomAD database, including 3,224 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001040458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERAP1 | NM_001040458.3 | c.166G>A | p.Glu56Lys | missense_variant | 2/19 | ENST00000443439.7 | NP_001035548.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERAP1 | ENST00000443439.7 | c.166G>A | p.Glu56Lys | missense_variant | 2/19 | 1 | NM_001040458.3 | ENSP00000406304.2 |
Frequencies
GnomAD3 genomes AF: 0.0588 AC: 8940AN: 152088Hom.: 356 Cov.: 32
GnomAD3 exomes AF: 0.0706 AC: 17749AN: 251488Hom.: 958 AF XY: 0.0650 AC XY: 8828AN XY: 135916
GnomAD4 exome AF: 0.0525 AC: 76685AN: 1461878Hom.: 2864 Cov.: 39 AF XY: 0.0515 AC XY: 37439AN XY: 727238
GnomAD4 genome AF: 0.0588 AC: 8948AN: 152206Hom.: 360 Cov.: 32 AF XY: 0.0621 AC XY: 4619AN XY: 74424
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at