chrX-23671600-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006406.2(PRDX4):c.313G>A(p.Asp105Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,205,613 control chromosomes in the GnomAD database, including 20 homozygotes. There are 456 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0072 ( 11 hom., 212 hem., cov: 23)
Exomes 𝑓: 0.00083 ( 9 hom. 244 hem. )
Consequence
PRDX4
NM_006406.2 missense
NM_006406.2 missense
Scores
3
5
7
Clinical Significance
Conservation
PhyloP100: 9.60
Genes affected
PRDX4 (HGNC:17169): (peroxiredoxin 4) The protein encoded by this gene is an antioxidant enzyme and belongs to the peroxiredoxin family. The protein is localized to the cytoplasm. Peroxidases of the peroxiredoxin family reduce hydrogen peroxide and alkyl hydroperoxides to water and alcohol with the use of reducing equivalents derived from thiol-containing donor molecules. This protein has been found to play a regulatory role in the activation of the transcription factor NF-kappaB. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009811461).
BP6
?
Variant X-23671600-G-A is Benign according to our data. Variant chrX-23671600-G-A is described in ClinVar as [Benign]. Clinvar id is 784430.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00722 (811/112354) while in subpopulation AFR AF= 0.0249 (773/30997). AF 95% confidence interval is 0.0235. There are 11 homozygotes in gnomad4. There are 212 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDX4 | NM_006406.2 | c.313G>A | p.Asp105Asn | missense_variant | 2/7 | ENST00000379341.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDX4 | ENST00000379341.9 | c.313G>A | p.Asp105Asn | missense_variant | 2/7 | 1 | NM_006406.2 | P1 | |
PRDX4 | ENST00000379331.3 | c.313G>A | p.Asp105Asn | missense_variant | 2/3 | 2 | |||
PRDX4 | ENST00000379349.5 | c.271G>A | p.Asp91Asn | missense_variant | 2/4 | 3 | |||
PRDX4 | ENST00000495599.1 | n.425G>A | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00722 AC: 811AN: 112301Hom.: 11 Cov.: 23 AF XY: 0.00616 AC XY: 212AN XY: 34429
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GnomAD3 exomes AF: 0.00196 AC: 345AN: 175936Hom.: 5 AF XY: 0.000903 AC XY: 55AN XY: 60938
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GnomAD4 exome AF: 0.000831 AC: 908AN: 1093259Hom.: 9 Cov.: 29 AF XY: 0.000679 AC XY: 244AN XY: 359091
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GnomAD4 genome ? AF: 0.00722 AC: 811AN: 112354Hom.: 11 Cov.: 23 AF XY: 0.00615 AC XY: 212AN XY: 34492
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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 | Feb 25, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;T;T
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.71
.;P;.
Vest4
0.75, 0.75
MVP
MPC
1.7
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at