rs420038
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021977.4(SLC22A3):c.430-10863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,148 control chromosomes in the GnomAD database, including 5,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5086 hom., cov: 33)
Consequence
SLC22A3
NM_021977.4 intron
NM_021977.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.149
Publications
14 publications found
Genes affected
SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 6-160387116-C-T is Benign according to our data. Variant chr6-160387116-C-T is described in ClinVar as Benign. ClinVar VariationId is 1285845.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_021977.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes 0.250 AC: 37950AN: 152030Hom.: 5083 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
37950
AN:
152030
Hom.:
Cov.:
33
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 0.250 AC: 37969AN: 152148Hom.: 5086 Cov.: 33 AF XY: 0.253 AC XY: 18785AN XY: 74382 show subpopulations
GnomAD4 genome
AF:
AC:
37969
AN:
152148
Hom.:
Cov.:
33
AF XY:
AC XY:
18785
AN XY:
74382
show subpopulations
African (AFR)
AF:
AC:
6846
AN:
41538
American (AMR)
AF:
AC:
3000
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
1224
AN:
3468
East Asian (EAS)
AF:
AC:
1904
AN:
5150
South Asian (SAS)
AF:
AC:
1788
AN:
4820
European-Finnish (FIN)
AF:
AC:
3095
AN:
10576
Middle Eastern (MID)
AF:
AC:
79
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19287
AN:
67982
Other (OTH)
AF:
AC:
567
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1501
3003
4504
6006
7507
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
400
800
1200
1600
2000
<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:
1241
AN:
3478
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational 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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.