chr4-9954455-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020041.3(SLC2A9):​c.682-12410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,322 control chromosomes in the GnomAD database, including 2,190 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 0.16 ( 2190 hom., cov: 34)

Consequence

SLC2A9
NM_020041.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

31 publications found
Variant links:
Genes affected
SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
SLC2A9 Gene-Disease associations (from GenCC):
  • hypouricemia, renal, 2
    Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • hereditary renal hypouricemia
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A9NM_020041.3 linkc.682-12410G>A intron_variant Intron 5 of 11 ENST00000264784.8 NP_064425.2 Q9NRM0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC2A9ENST00000264784.8 linkc.682-12410G>A intron_variant Intron 5 of 11 1 NM_020041.3 ENSP00000264784.3 Q9NRM0-1
SLC2A9ENST00000309065.7 linkc.595-12410G>A intron_variant Intron 6 of 12 1 ENSP00000311383.3 Q9NRM0-2
SLC2A9ENST00000505104.5 linkn.716-12410G>A intron_variant Intron 6 of 11 1
SLC2A9ENST00000506583.5 linkc.595-12410G>A intron_variant Intron 7 of 13 5 ENSP00000422209.1 Q9NRM0-2

Frequencies

GnomAD3 genomes
AF:
0.160
AC:
24391
AN:
152204
Hom.:
2187
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0943
Gnomad AMI
AF:
0.139
Gnomad AMR
AF:
0.226
Gnomad ASJ
AF:
0.251
Gnomad EAS
AF:
0.0156
Gnomad SAS
AF:
0.168
Gnomad FIN
AF:
0.173
Gnomad MID
AF:
0.171
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.166
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.160
AC:
24402
AN:
152322
Hom.:
2190
Cov.:
34
AF XY:
0.160
AC XY:
11951
AN XY:
74474
show subpopulations
African (AFR)
AF:
0.0941
AC:
3912
AN:
41586
American (AMR)
AF:
0.226
AC:
3464
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.251
AC:
872
AN:
3472
East Asian (EAS)
AF:
0.0158
AC:
82
AN:
5184
South Asian (SAS)
AF:
0.169
AC:
816
AN:
4834
European-Finnish (FIN)
AF:
0.173
AC:
1834
AN:
10612
Middle Eastern (MID)
AF:
0.167
AC:
49
AN:
294
European-Non Finnish (NFE)
AF:
0.190
AC:
12900
AN:
68014
Other (OTH)
AF:
0.164
AC:
347
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1066
2131
3197
4262
5328
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
268
536
804
1072
1340
<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:
0.177
Hom.:
7309
Bravo
AF:
0.160
Asia WGS
AF:
0.0950
AC:
331
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.4
DANN
Benign
0.51
PhyloP100
-0.23
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: rs4481233; hg19: chr4-9956079; API