rs2301365
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000572173.1(RMI2):c.-515-13787G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 644,152 control chromosomes in the GnomAD database, including 18,926 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3926 hom., cov: 33)
Exomes 𝑓: 0.24 ( 15000 hom. )
Consequence
RMI2
ENST00000572173.1 intron
ENST00000572173.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.956
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 16-11281429-G-T is Benign according to our data. Variant chr16-11281429-G-T is described in ClinVar as [Benign]. Clinvar id is 1223123.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105371082 | XR_933070.4 | n.178+31651G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RMI2 | ENST00000572173.1 | c.-515-13787G>T | intron_variant | 1 | |||||
RMI2 | ENST00000573910.1 | n.160+31651G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
RMI2 | ENST00000649869.1 | n.152+31651G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.215 AC: 32640AN: 152042Hom.: 3928 Cov.: 33
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GnomAD4 exome AF: 0.239 AC: 117650AN: 491992Hom.: 15000 AF XY: 0.237 AC XY: 62048AN XY: 261816
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GnomAD4 genome ? AF: 0.214 AC: 32627AN: 152160Hom.: 3926 Cov.: 33 AF XY: 0.214 AC XY: 15910AN XY: 74376
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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 | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 27216534, 18390561) - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at