4-10019527-G-A

Variant summary

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

The NM_020041.3(SLC2A9):​c.151-454C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,268 control chromosomes in the GnomAD database, including 1,427 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 0.10 ( 1427 hom., cov: 33)

Consequence

SLC2A9
NM_020041.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC2A9NM_020041.3 linkuse as main transcriptc.151-454C>T intron_variant ENST00000264784.8 NP_064425.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC2A9ENST00000264784.8 linkuse as main transcriptc.151-454C>T intron_variant 1 NM_020041.3 ENSP00000264784 A2Q9NRM0-1

Frequencies

GnomAD3 genomes
AF:
0.103
AC:
15694
AN:
152150
Hom.:
1413
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.100
Gnomad ASJ
AF:
0.0703
Gnomad EAS
AF:
0.461
Gnomad SAS
AF:
0.161
Gnomad FIN
AF:
0.0726
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.0367
Gnomad OTH
AF:
0.0908
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.103
AC:
15744
AN:
152268
Hom.:
1427
Cov.:
33
AF XY:
0.107
AC XY:
7987
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.175
Gnomad4 AMR
AF:
0.100
Gnomad4 ASJ
AF:
0.0703
Gnomad4 EAS
AF:
0.460
Gnomad4 SAS
AF:
0.162
Gnomad4 FIN
AF:
0.0726
Gnomad4 NFE
AF:
0.0367
Gnomad4 OTH
AF:
0.0951
Alfa
AF:
0.0621
Hom.:
268
Bravo
AF:
0.110
Asia WGS
AF:
0.275
AC:
953
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.2
DANN
Benign
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs2240723; hg19: chr4-10021151; API