rs17149866
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001134405.2(RUNDC3B):c.372+4971T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 152,360 control chromosomes in the GnomAD database, including 6 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 0.0031 ( 6 hom., cov: 32)
Consequence
RUNDC3B
NM_001134405.2 intron
NM_001134405.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.104
Publications
2 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]
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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=-0.78).
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00312 (475/152360) while in subpopulation EAS AF = 0.0492 (255/5188). AF 95% confidence interval is 0.0442. There are 6 homozygotes in GnomAd4. There are 249 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 6 Unknown gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 473AN: 152240Hom.: 6 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
473
AN:
152240
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: 0.00312 AC: 475AN: 152360Hom.: 6 Cov.: 32 AF XY: 0.00334 AC XY: 249AN XY: 74516 show subpopulations
GnomAD4 genome
AF:
AC:
475
AN:
152360
Hom.:
Cov.:
32
AF XY:
AC XY:
249
AN XY:
74516
show subpopulations
African (AFR)
AF:
AC:
79
AN:
41594
American (AMR)
AF:
AC:
97
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3472
East Asian (EAS)
AF:
AC:
255
AN:
5188
South Asian (SAS)
AF:
AC:
12
AN:
4828
European-Finnish (FIN)
AF:
AC:
1
AN:
10624
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
17
AN:
68026
Other (OTH)
AF:
AC:
12
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
23
46
69
92
115
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
62
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
Publications
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