NM_021977.4:c.429+5698G>T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

21 publications found
Variant links:
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 -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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC22A3NM_021977.4 linkc.429+5698G>T intron_variant Intron 1 of 10 ENST00000275300.3 NP_068812.1 O75751

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC22A3ENST00000275300.3 linkc.429+5698G>T intron_variant Intron 1 of 10 1 NM_021977.4 ENSP00000275300.2 O75751

Frequencies

GnomAD3 genomes
AF:
0.501
AC:
76035
AN:
151854
Hom.:
19356
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.590
Gnomad AMI
AF:
0.384
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.544
Gnomad EAS
AF:
0.299
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.497
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.488
Gnomad OTH
AF:
0.491
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.501
AC:
76125
AN:
151974
Hom.:
19392
Cov.:
32
AF XY:
0.498
AC XY:
36988
AN XY:
74262
show subpopulations
African (AFR)
AF:
0.590
AC:
24442
AN:
41414
American (AMR)
AF:
0.429
AC:
6552
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.544
AC:
1886
AN:
3466
East Asian (EAS)
AF:
0.299
AC:
1547
AN:
5166
South Asian (SAS)
AF:
0.364
AC:
1752
AN:
4810
European-Finnish (FIN)
AF:
0.497
AC:
5242
AN:
10544
Middle Eastern (MID)
AF:
0.507
AC:
149
AN:
294
European-Non Finnish (NFE)
AF:
0.488
AC:
33169
AN:
67976
Other (OTH)
AF:
0.491
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:
0.487
Hom.:
5101
Bravo
AF:
0.505
Asia WGS
AF:
0.362
AC:
1261
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.24
DANN
Benign
0.37
PhyloP100
-2.2
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs518295; hg19: chr6-160775578; API