chr16-11288838-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000572173.1(RMI2):c.-515-6378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,202 control chromosomes in the GnomAD database, including 2,313 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 0.17 ( 2313 hom., cov: 32)
Consequence
RMI2
ENST00000572173.1 intron
ENST00000572173.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.967
Publications
9 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105371082 | XR_933070.4 | n.178+39060C>T | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RMI2 | ENST00000572173.1 | c.-515-6378C>T | intron_variant | Intron 1 of 4 | 1 | ENSP00000461206.1 | ||||
RMI2 | ENST00000573910.1 | n.161-27614C>T | intron_variant | Intron 1 of 1 | 3 | |||||
RMI2 | ENST00000649869.1 | n.152+39060C>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.173 AC: 26246AN: 152084Hom.: 2308 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
26246
AN:
152084
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.173 AC: 26268AN: 152202Hom.: 2313 Cov.: 32 AF XY: 0.167 AC XY: 12443AN XY: 74410 show subpopulations
GnomAD4 genome
AF:
AC:
26268
AN:
152202
Hom.:
Cov.:
32
AF XY:
AC XY:
12443
AN XY:
74410
show subpopulations
African (AFR)
AF:
AC:
7923
AN:
41540
American (AMR)
AF:
AC:
1829
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
504
AN:
3468
East Asian (EAS)
AF:
AC:
244
AN:
5174
South Asian (SAS)
AF:
AC:
613
AN:
4824
European-Finnish (FIN)
AF:
AC:
1586
AN:
10602
Middle Eastern (MID)
AF:
AC:
22
AN:
294
European-Non Finnish (NFE)
AF:
AC:
13085
AN:
67984
Other (OTH)
AF:
AC:
296
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1130
2259
3389
4518
5648
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
296
592
888
1184
1480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
296
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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