Variant chr4-10018940-G-A 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.249+35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 1,543,166 control chromosomes in the GnomAD database, including 218,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16394 hom., cov: 34)

Exomes 𝑓: 0.54 ( 201787 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.519

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=-0.5).

BP6

Variant 4-10018940-G-A is Benign according to our data. Variant chr4-10018940-G-A is described in ClinVar as [Benign]. Clinvar id is 1234312.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.249+35C>T		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.249+35C>T		intron_variant		1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67013

AN:

152050

Hom.:

16386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.498

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.452

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.457

GnomAD3 exomes

AF:

0.521

AC:

77227

AN:

148358

Hom.:

20781

AF XY:

0.528

AC XY:

41762

AN XY:

79044

show subpopulations

Gnomad AFR exome

AF:

0.194

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.515

Gnomad EAS exome

AF:

0.424

Gnomad SAS exome

AF:

0.602

Gnomad FIN exome

AF:

0.531

Gnomad NFE exome

AF:

0.543

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.535

AC:

744282

AN:

1390996

Hom.:

201787

Cov.:

AF XY:

0.538

AC XY:

368999

AN XY:

686340

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.523

Gnomad4 ASJ exome

AF:

0.516

Gnomad4 EAS exome

AF:

0.436

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.546

Gnomad4 OTH exome

AF:

0.507

GnomAD4 genome

AF:

0.441

AC:

67031

AN:

152170

Hom.:

16394

Cov.:

AF XY:

0.443

AC XY:

32952

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.498

Gnomad4 EAS

AF:

0.421

Gnomad4 SAS

AF:

0.587

Gnomad4 FIN

AF:

0.525

Gnomad4 NFE

AF:

0.542

Gnomad4 OTH

AF:

0.457

Alfa

AF:

0.491

Hom.:

3536

Bravo

AF:

0.427

Asia WGS

AF:

0.508

AC:

1764

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hypouricemia, renal, 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

8.1

DANN

Benign

0.96

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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