NM_021977.4:c.429+5698G>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021977.4(SLC22A3):c.429+5698G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,974 control chromosomes in the GnomAD database, including 19,392 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 0.50 ( 19392 hom., cov: 32)
Consequence
SLC22A3
NM_021977.4 intron
NM_021977.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.18
Publications
21 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]
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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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.501 AC: 76035AN: 151854Hom.: 19356 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
76035
AN:
151854
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: 0.501 AC: 76125AN: 151974Hom.: 19392 Cov.: 32 AF XY: 0.498 AC XY: 36988AN XY: 74262 show subpopulations
GnomAD4 genome
AF:
AC:
76125
AN:
151974
Hom.:
Cov.:
32
AF XY:
AC XY:
36988
AN XY:
74262
show subpopulations
African (AFR)
AF:
AC:
24442
AN:
41414
American (AMR)
AF:
AC:
6552
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
1886
AN:
3466
East Asian (EAS)
AF:
AC:
1547
AN:
5166
South Asian (SAS)
AF:
AC:
1752
AN:
4810
European-Finnish (FIN)
AF:
AC:
5242
AN:
10544
Middle Eastern (MID)
AF:
AC:
149
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33169
AN:
67976
Other (OTH)
AF:
AC:
1037
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1930
3861
5791
7722
9652
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
662
1324
1986
2648
3310
<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:
1261
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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