2-171553387-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000321348.9(CYBRD1):c.444G>A(p.Pro148=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,613,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
CYBRD1
ENST00000321348.9 synonymous
ENST00000321348.9 synonymous
Scores
15
Clinical Significance
Conservation
PhyloP100: -0.0610
Genes affected
CYBRD1 (HGNC:20797): (cytochrome b reductase 1) This gene is a member of the cytochrome b(561) family that encodes an iron-regulated protein. It highly expressed in the duodenal brush border membrane. It has ferric reductase activity and is believed to play a physiological role in dietary iron absorption. [provided by RefSeq, Jul 2008]
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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 (MetaRNN=0.009544402).
BP6
Variant 2-171553387-G-A is Benign according to our data. Variant chr2-171553387-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3079297.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.061 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYBRD1 | NM_024843.4 | c.444G>A | p.Pro148= | synonymous_variant | 3/4 | ENST00000321348.9 | NP_079119.3 | |
CYBRD1 | NM_001127383.2 | c.235G>A | p.Ala79Thr | missense_variant | 2/3 | NP_001120855.1 | ||
CYBRD1 | NM_001256909.2 | c.270G>A | p.Pro90= | synonymous_variant | 3/4 | NP_001243838.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYBRD1 | ENST00000375252.3 | c.235G>A | p.Ala79Thr | missense_variant | 2/3 | 1 | ENSP00000364401 | |||
CYBRD1 | ENST00000321348.9 | c.444G>A | p.Pro148= | synonymous_variant | 3/4 | 1 | NM_024843.4 | ENSP00000319141 | P1 | |
CYBRD1 | ENST00000409484.5 | c.270G>A | p.Pro90= | synonymous_variant | 3/4 | 2 | ENSP00000386739 | |||
CYBRD1 | ENST00000445146.1 | c.327G>A | p.Pro109= | synonymous_variant | 3/4 | 3 | ENSP00000402242 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152098Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000147 AC: 37AN: 251016Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135648
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GnomAD4 exome AF: 0.000125 AC: 182AN: 1461316Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 726970
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GnomAD4 genome AF: 0.000237 AC: 36AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74422
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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