chr22-32225632-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014227.3(SLC5A4):c.1449+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 1,534,040 control chromosomes in the GnomAD database, including 166,117 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 0.51 ( 21069 hom., cov: 32)
Exomes 𝑓: 0.45 ( 145048 hom. )
Consequence
SLC5A4
NM_014227.3 intron
NM_014227.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.17
Publications
12 publications found
Genes affected
SLC5A4 (HGNC:11039): (solute carrier family 5 member 4) Predicted to enable glucose:sodium symporter activity and proton transmembrane transporter activity. Predicted to be involved in sodium ion transport. Predicted to act upstream of or within proton transmembrane transport. Predicted to be active in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A4 | ENST00000266086.6 | c.1449+23G>A | intron_variant | Intron 12 of 14 | 1 | NM_014227.3 | ENSP00000266086.3 | |||
SLC5A4-AS1 | ENST00000434942.2 | n.225-3458C>T | intron_variant | Intron 2 of 4 | 3 | |||||
SLC5A4-AS1 | ENST00000452181.2 | n.274+18356C>T | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.507 AC: 76908AN: 151834Hom.: 21027 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
76908
AN:
151834
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:
GnomAD2 exomes AF: 0.424 AC: 89678AN: 211306 AF XY: 0.426 show subpopulations
GnomAD2 exomes
AF:
AC:
89678
AN:
211306
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.451 AC: 623226AN: 1382088Hom.: 145048 Cov.: 22 AF XY: 0.449 AC XY: 308359AN XY: 686826 show subpopulations
GnomAD4 exome
AF:
AC:
623226
AN:
1382088
Hom.:
Cov.:
22
AF XY:
AC XY:
308359
AN XY:
686826
show subpopulations
African (AFR)
AF:
AC:
21533
AN:
29924
American (AMR)
AF:
AC:
10967
AN:
34420
Ashkenazi Jewish (ASJ)
AF:
AC:
10208
AN:
23916
East Asian (EAS)
AF:
AC:
4725
AN:
38144
South Asian (SAS)
AF:
AC:
30613
AN:
76188
European-Finnish (FIN)
AF:
AC:
21654
AN:
52372
Middle Eastern (MID)
AF:
AC:
2523
AN:
5508
European-Non Finnish (NFE)
AF:
AC:
495045
AN:
1064418
Other (OTH)
AF:
AC:
25958
AN:
57198
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.474
Heterozygous variant carriers
0
14085
28170
42255
56340
70425
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
14792
29584
44376
59168
73960
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.507 AC: 77013AN: 151952Hom.: 21069 Cov.: 32 AF XY: 0.499 AC XY: 37039AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
77013
AN:
151952
Hom.:
Cov.:
32
AF XY:
AC XY:
37039
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
29447
AN:
41450
American (AMR)
AF:
AC:
5955
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
1550
AN:
3468
East Asian (EAS)
AF:
AC:
743
AN:
5180
South Asian (SAS)
AF:
AC:
1893
AN:
4818
European-Finnish (FIN)
AF:
AC:
4302
AN:
10542
Middle Eastern (MID)
AF:
AC:
133
AN:
292
European-Non Finnish (NFE)
AF:
AC:
31544
AN:
67898
Other (OTH)
AF:
AC:
971
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1800
3600
5400
7200
9000
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
658
1316
1974
2632
3290
<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:
1200
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.