11-4129084-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2PP3
The NM_001033.5(RRM1):c.1703A>G(p.Tyr568Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000442 in 1,585,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
RRM1
NM_001033.5 missense
NM_001033.5 missense
Scores
9
8
2
Clinical Significance
Conservation
PhyloP100: 8.92
Genes affected
RRM1 (HGNC:10451): (ribonucleotide reductase catalytic subunit M1) This gene encodes the large and catalytic subunit of ribonucleotide reductase, an enzyme essential for the conversion of ribonucleotides into deoxyribonucleotides. A pool of available deoxyribonucleotides is important for DNA replication during S phase of the cell cycle as well as multiple DNA repair processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, RRM1
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.807
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RRM1 | NM_001033.5 | c.1703A>G | p.Tyr568Cys | missense_variant | 15/19 | ENST00000300738.10 | |
RRM1 | NM_001318064.1 | c.1412A>G | p.Tyr471Cys | missense_variant | 14/18 | ||
RRM1 | NM_001330193.1 | c.1037A>G | p.Tyr346Cys | missense_variant | 9/13 | ||
RRM1 | NM_001318065.1 | c.689A>G | p.Tyr230Cys | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RRM1 | ENST00000300738.10 | c.1703A>G | p.Tyr568Cys | missense_variant | 15/19 | 1 | NM_001033.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000667 AC: 1AN: 149910Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000418 AC: 6AN: 1435448Hom.: 0 Cov.: 26 AF XY: 0.00000280 AC XY: 2AN XY: 715310
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GnomAD4 genome ? AF: 0.00000667 AC: 1AN: 149910Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 72936
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.1703A>G (p.Y568C) alteration is located in exon 15 (coding exon 15) of the RRM1 gene. This alteration results from a A to G substitution at nucleotide position 1703, causing the tyrosine (Y) at amino acid position 568 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
H;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Loss of phosphorylation at Y568 (P = 0.0543);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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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