chr4-10042064-C-T

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-1800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,932 control chromosomes in the GnomAD database, including 10,224 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 0.34 ( 10224 hom., cov: 32)

Consequence

SLC2A9
ENST00000506583.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC2A9ENST00000506583.5 linkuse as main transcriptc.-175-1800G>A intron_variant 5 P2Q9NRM0-2
SLC2A9ENST00000513129.1 linkuse as main transcriptc.-41+12769G>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.336
AC:
50966
AN:
151814
Hom.:
10201
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.556
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.215
Gnomad EAS
AF:
0.0929
Gnomad SAS
AF:
0.0921
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.280
Gnomad OTH
AF:
0.314
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.336
AC:
51019
AN:
151932
Hom.:
10224
Cov.:
32
AF XY:
0.329
AC XY:
24419
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.556
Gnomad4 AMR
AF:
0.229
Gnomad4 ASJ
AF:
0.215
Gnomad4 EAS
AF:
0.0935
Gnomad4 SAS
AF:
0.0912
Gnomad4 FIN
AF:
0.276
Gnomad4 NFE
AF:
0.280
Gnomad4 OTH
AF:
0.311
Alfa
AF:
0.324
Hom.:
1095
Bravo
AF:
0.344
Asia WGS
AF:
0.131
AC:
463
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
12
DANN
Benign
0.90

Splicing

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: rs6850166; hg19: chr4-10043688; API