rs2032933
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152308.3(RMI2):c.*393G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 238,306 control chromosomes in the GnomAD database, including 84,247 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.84 ( 53746 hom., cov: 33)
Exomes 𝑓: 0.84 ( 30501 hom. )
Consequence
RMI2
NM_152308.3 3_prime_UTR
NM_152308.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.49
Genes affected
RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RMI2 | NM_152308.3 | c.*393G>A | 3_prime_UTR_variant | 2/2 | ENST00000312499.6 | ||
LOC105371082 | XR_933070.4 | n.179-28639G>A | intron_variant, non_coding_transcript_variant | ||||
RMI2 | NR_130754.2 | n.627G>A | non_coding_transcript_exon_variant | 2/2 | |||
LOC105371082 | XR_933073.3 | n.810-28639G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RMI2 | ENST00000312499.6 | c.*393G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_152308.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.840 AC: 127703AN: 152096Hom.: 53696 Cov.: 33
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GnomAD4 exome AF: 0.840 AC: 72323AN: 86092Hom.: 30501 Cov.: 0 AF XY: 0.839 AC XY: 33656AN XY: 40112
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GnomAD4 genome ? AF: 0.840 AC: 127811AN: 152214Hom.: 53746 Cov.: 33 AF XY: 0.845 AC XY: 62900AN XY: 74396
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at