chr5-96879768-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022350.5(ERAP2):āc.83T>Cā(p.Ile28Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022350.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERAP2 | NM_022350.5 | c.83T>C | p.Ile28Thr | missense_variant | 2/19 | ENST00000437043.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERAP2 | ENST00000437043.8 | c.83T>C | p.Ile28Thr | missense_variant | 2/19 | 1 | NM_022350.5 | P1 | |
ENST00000501338.5 | n.1689-6390A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251146Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135714
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.83T>C (p.I28T) alteration is located in exon 2 (coding exon 1) of the ERAP2 gene. This alteration results from a T to C substitution at nucleotide position 83, causing the isoleucine (I) at amino acid position 28 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at