Variant 4-10021256-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020041.3(SLC2A9):c.150+24A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 1,611,592 control chromosomes in the GnomAD database, including 5,913 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 821 hom., cov: 33)

Exomes 𝑓: 0.051 ( 5092 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.972

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 4-10021256-T-C is Benign according to our data. Variant chr4-10021256-T-C is described in ClinVar as [Benign]. Clinvar id is 1241111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.150+24A>G		intron_variant		ENST00000264784.8	NP_064425.2	Q9NRM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8 link	c.150+24A>G		intron_variant		1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.0769

AC:

11708

AN:

152168

Hom.:

817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0891

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.390

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0557

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0308

Gnomad OTH

AF:

0.0686

GnomAD3 exomes

AF:

0.0875

AC:

21855

AN:

249666

Hom.:

2068

AF XY:

0.0830

AC XY:

11211

AN XY:

135060

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.112

Gnomad ASJ exome

AF:

0.0648

Gnomad EAS exome

AF:

0.397

Gnomad SAS exome

AF:

0.0961

Gnomad FIN exome

AF:

0.0550

Gnomad NFE exome

AF:

0.0322

Gnomad OTH exome

AF:

0.0705

GnomAD4 exome

AF:

0.0511

AC:

74512

AN:

1459308

Hom.:

5092

Cov.:

AF XY:

0.0518

AC XY:

37581

AN XY:

726064

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.112

Gnomad4 ASJ exome

AF:

0.0622

Gnomad4 EAS exome

AF:

0.399

Gnomad4 SAS exome

AF:

0.0981

Gnomad4 FIN exome

AF:

0.0554

Gnomad4 NFE exome

AF:

0.0289

Gnomad4 OTH exome

AF:

0.0683

GnomAD4 genome

AF:

0.0771

AC:

11734

AN:

152284

Hom.:

821

Cov.:

AF XY:

0.0806

AC XY:

6000

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.0891

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.389

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.0557

Gnomad4 NFE

AF:

0.0308

Gnomad4 OTH

AF:

0.0716

Alfa

AF:

0.0596

Hom.:

101

Bravo

AF:

0.0830

Asia WGS

AF:

0.206

AC:

716

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 18, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.2

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over