NM_006446.5:c.727+3236C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006446.5(SLCO1B1):c.727+3236C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,898 control chromosomes in the GnomAD database, including 12,812 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 0.37 ( 12812 hom., cov: 31)
Consequence
SLCO1B1
NM_006446.5 intron
NM_006446.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.249
Publications
6 publications found
Genes affected
SLCO1B1 (HGNC:10959): (solute carrier organic anion transporter family member 1B1) This gene encodes a liver-specific member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of numerous endogenous compounds including bilirubin, 17-beta-glucuronosyl estradiol and leukotriene C4. This protein is also involved in the removal of drug compounds such as statins, bromosulfophthalein and rifampin from the blood into the hepatocytes. Polymorphisms in the gene encoding this protein are associated with impaired transporter function. [provided by RefSeq, Mar 2009]
SLCO1B1 Gene-Disease associations (from GenCC):
- Rotor syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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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=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B1 | NM_006446.5 | c.727+3236C>G | intron_variant | Intron 7 of 14 | ENST00000256958.3 | NP_006437.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.373 AC: 56596AN: 151778Hom.: 12808 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
56596
AN:
151778
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 AF: 0.373 AC: 56598AN: 151898Hom.: 12812 Cov.: 31 AF XY: 0.374 AC XY: 27730AN XY: 74210 show subpopulations
GnomAD4 genome
AF:
AC:
56598
AN:
151898
Hom.:
Cov.:
31
AF XY:
AC XY:
27730
AN XY:
74210
show subpopulations
African (AFR)
AF:
AC:
4520
AN:
41494
American (AMR)
AF:
AC:
6975
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
AC:
1575
AN:
3466
East Asian (EAS)
AF:
AC:
1296
AN:
5132
South Asian (SAS)
AF:
AC:
2624
AN:
4810
European-Finnish (FIN)
AF:
AC:
4620
AN:
10510
Middle Eastern (MID)
AF:
AC:
120
AN:
292
European-Non Finnish (NFE)
AF:
AC:
33816
AN:
67938
Other (OTH)
AF:
AC:
812
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1610
3220
4830
6440
8050
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
538
1076
1614
2152
2690
<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:
1247
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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