chr5-96896421-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_022350.5(ERAP2):āc.1288T>Cā(p.Leu430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,612,798 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0012 ( 0 hom., cov: 31)
Exomes š: 0.00013 ( 1 hom. )
Consequence
ERAP2
NM_022350.5 synonymous
NM_022350.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0910
Genes affected
ERAP2 (HGNC:29499): (endoplasmic reticulum aminopeptidase 2) This gene encodes a zinc metalloaminopeptidase of the M1 protease family that resides in the endoplasmic reticulum and functions in N-terminal trimming antigenic epitopes for presentation by major histocompatibility complex (MHC) class I molecules. Certain mutations in this gene are associated with the inflammatory arthritis syndrome ankylosing spondylitis and pre-eclampsia. This gene is located adjacent to a closely related aminopeptidase gene on chromosome 5. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 5-96896421-T-C is Benign according to our data. Variant chr5-96896421-T-C is described in ClinVar as [Benign]. Clinvar id is 727215.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.091 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERAP2 | NM_022350.5 | c.1288T>C | p.Leu430= | synonymous_variant | 8/19 | ENST00000437043.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERAP2 | ENST00000437043.8 | c.1288T>C | p.Leu430= | synonymous_variant | 8/19 | 1 | NM_022350.5 | P1 | |
ENST00000501338.5 | n.1689-23043A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00119 AC: 181AN: 152198Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000279 AC: 70AN: 250768Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135582
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GnomAD4 exome AF: 0.000127 AC: 186AN: 1460482Hom.: 1 Cov.: 29 AF XY: 0.000127 AC XY: 92AN XY: 726588
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GnomAD4 genome AF: 0.00120 AC: 183AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.00122 AC XY: 91AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at