chr4-9995488-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020041.3(SLC2A9):​c.410+1293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,084 control chromosomes in the GnomAD database, including 38,876 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 0.71 ( 38876 hom., cov: 31)

Consequence

SLC2A9
NM_020041.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84
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-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC2A9NM_020041.3 linkc.410+1293G>T intron_variant Intron 3 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.410+1293G>T intron_variant Intron 3 of 11 1 NM_020041.3 ENSP00000264784.3 Q9NRM0-1

Frequencies

GnomAD3 genomes
AF:
0.713
AC:
108418
AN:
151966
Hom.:
38860
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.688
Gnomad AMI
AF:
0.799
Gnomad AMR
AF:
0.659
Gnomad ASJ
AF:
0.657
Gnomad EAS
AF:
0.584
Gnomad SAS
AF:
0.675
Gnomad FIN
AF:
0.734
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.752
Gnomad OTH
AF:
0.718
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.713
AC:
108477
AN:
152084
Hom.:
38876
Cov.:
31
AF XY:
0.709
AC XY:
52703
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.688
Gnomad4 AMR
AF:
0.659
Gnomad4 ASJ
AF:
0.657
Gnomad4 EAS
AF:
0.584
Gnomad4 SAS
AF:
0.674
Gnomad4 FIN
AF:
0.734
Gnomad4 NFE
AF:
0.752
Gnomad4 OTH
AF:
0.717
Alfa
AF:
0.685
Hom.:
6506
Bravo
AF:
0.707
Asia WGS
AF:
0.671
AC:
2332
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.37
DANN
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4529048; hg19: chr4-9997112; API