Genetic Variant SLC2A9:c.681+25G>A (chr4-9980567-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_020041.3(SLC2A9):c.681+25G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,613,260 control chromosomes in the GnomAD database, including 205,376 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14795 hom., cov: 33)

Exomes 𝑓: 0.51 ( 190581 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.92

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=-0.86).

BP6

Variant 4-9980567-C-T is Benign according to our data. Variant chr4-9980567-C-T is described in ClinVar as [Benign]. Clinvar id is 1287173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.681+25G>A		intron_variant	Intron 5 of 11	ENST00000264784.8	NP_064425.2	Q9NRM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8 link	c.681+25G>A		intron_variant	Intron 5 of 11	1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.422

AC:

64153

AN:

151930

Hom.:

14788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.441

GnomAD3 exomes

AF:

0.472

AC:

118272

AN:

250514

Hom.:

28951

AF XY:

0.482

AC XY:

65377

AN XY:

135554

show subpopulations

Gnomad AFR exome

AF:

0.215

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.525

Gnomad EAS exome

AF:

0.424

Gnomad SAS exome

AF:

0.511

Gnomad FIN exome

AF:

0.521

Gnomad NFE exome

AF:

0.520

Gnomad OTH exome

AF:

0.492

GnomAD4 exome

AF:

0.507

AC:

741096

AN:

1461212

Hom.:

190581

Cov.:

AF XY:

0.509

AC XY:

369771

AN XY:

726934

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.377

Gnomad4 ASJ exome

AF:

0.525

Gnomad4 EAS exome

AF:

0.431

Gnomad4 SAS exome

AF:

0.510

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.524

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.422

AC:

64158

AN:

152048

Hom.:

14795

Cov.:

AF XY:

0.423

AC XY:

31420

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.223

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.509

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.507

Gnomad4 FIN

AF:

0.516

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.465

Hom.:

3475

Bravo

AF:

0.405

Asia WGS

AF:

0.465

AC:

1615

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypouricemia, renal, 2

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.0090

DANN

Benign

0.59

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