2-10122846-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001034.4(RRM2):c.48G>A(p.Gln16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,602,314 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 4 hom. )
Consequence
RRM2
NM_001034.4 synonymous
NM_001034.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.197
Genes affected
RRM2 (HGNC:10452): (ribonucleotide reductase regulatory subunit M2) This gene encodes one of two non-identical subunits for ribonucleotide reductase. This reductase catalyzes the formation of deoxyribonucleotides from ribonucleotides. Synthesis of the encoded protein (M2) is regulated in a cell-cycle dependent fashion. Transcription from this gene can initiate from alternative promoters, which results in two isoforms that differ in the lengths of their N-termini. Related pseudogenes have been identified on chromosomes 1 and X. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 2-10122846-G-A is Benign according to our data. Variant chr2-10122846-G-A is described in ClinVar as [Benign]. Clinvar id is 711013.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.197 with no splicing effect.
BS2
High AC in GnomAd4 at 246 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RRM2 | NM_001034.4 | c.48G>A | p.Gln16= | synonymous_variant | 1/10 | ENST00000304567.10 | |
RRM2 | NM_001165931.1 | c.228G>A | p.Gln76= | synonymous_variant | 1/10 | ||
RRM2 | NR_164157.1 | n.108G>A | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RRM2 | ENST00000304567.10 | c.48G>A | p.Gln16= | synonymous_variant | 1/10 | 1 | NM_001034.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00162 AC: 246AN: 152216Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00183 AC: 406AN: 222102Hom.: 0 AF XY: 0.00175 AC XY: 212AN XY: 121152
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GnomAD4 exome AF: 0.00228 AC: 3312AN: 1449980Hom.: 4 Cov.: 35 AF XY: 0.00220 AC XY: 1583AN XY: 720350
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GnomAD4 genome AF: 0.00161 AC: 246AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.00160 AC XY: 119AN XY: 74492
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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 | Jan 22, 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