chr7-87649444-G-A
Variant names:
Variant summary
Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
Benign
The NM_001134405.2(RUNDC3B):c.123-1378G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,082 control chromosomes in the GnomAD database, including 49,879 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 0.81 ( 49879 hom., cov: 31)
Consequence
RUNDC3B
NM_001134405.2 intron
NM_001134405.2 intron
Scores
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.380
Publications
17 publications found
Genes affected
RUNDC3B (HGNC:30286): (RUN domain containing 3B)
ABCB1 (HGNC:40): (ATP binding cassette subfamily B member 1) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is an ATP-dependent drug efflux pump for xenobiotic compounds with broad substrate specificity. It is responsible for decreased drug accumulation in multidrug-resistant cells and often mediates the development of resistance to anticancer drugs. This protein also functions as a transporter in the blood-brain barrier. Mutations in this gene are associated with colchicine resistance and Inflammatory bowel disease 13. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Feb 2017]
ABCB1 Gene-Disease associations (from GenCC):
- inflammatory bowel disease 13Inheritance: AD Classification: LIMITED Submitted by: PanelApp Australia
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new If you want to explore the variant's impact on the transcript NM_001134405.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001134405.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RUNDC3B | TSL:2 MANE Select | c.123-1378G>A | intron | N/A | ENSP00000378149.3 | Q96NL0-5 | |||
| ABCB1 | TSL:1 | c.-330-48366C>T | intron | N/A | ENSP00000265724.3 | P08183-1 | |||
| RUNDC3B | TSL:1 | c.123-1378G>A | intron | N/A | ENSP00000420394.1 | Q96NL0-4 |
Frequencies
GnomAD3 genomes 0.808 AC: 122726AN: 151964Hom.: 49827 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
122726
AN:
151964
Hom.:
Cov.:
31
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 0.808 AC: 122836AN: 152082Hom.: 49879 Cov.: 31 AF XY: 0.813 AC XY: 60437AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
122836
AN:
152082
Hom.:
Cov.:
31
AF XY:
AC XY:
60437
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
35010
AN:
41502
American (AMR)
AF:
AC:
12919
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
2708
AN:
3472
East Asian (EAS)
AF:
AC:
5115
AN:
5180
South Asian (SAS)
AF:
AC:
4247
AN:
4816
European-Finnish (FIN)
AF:
AC:
8474
AN:
10566
Middle Eastern (MID)
AF:
AC:
235
AN:
294
European-Non Finnish (NFE)
AF:
AC:
51868
AN:
67956
Other (OTH)
AF:
AC:
1691
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1196
2392
3589
4785
5981
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
878
1756
2634
3512
4390
<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:
3202
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs10267099 ;
hg19: chr7-87278760;