chr4-9920541-AAC-GAT

Variant names:

• chr4-9920541-AAC-GAT
• NM_020041.3:c.844_846delGTTinsATC
• SLC2A9 p.Val282Ile

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+1 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 1 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB2_Supporting

The NM_020041.3(SLC2A9):c.844_846delGTTinsATC (p.Val282Ile) variant causes a missense change. The gene SLC2A9 is a tumor suppressor gene (CancerMine: 2 TSG citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.V282I: Benign (ClinVar VariationId 350215, 2 stars) This exact variant is curated in the UniProt human variants database as Uncertain Significance; it is also listed as a COSMIC curated somatic variant.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC2A9 NM_020041.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.82
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• hypouricemia, renal, 2

  Inheritance: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
	B2Does not fit gene mode of action		Activating variant in tumor suppressor gene + same AA change classified germline Benign/Likely Benign — supporting benign evidence (B2, no cancer-type context); Activating variant in tumor suppressor gene + same AA change classified germline Benign/Likely Benign — supporting benign evidence (B2, no cancer-type context)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_020041.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	SLC2A9 NM_020041.3	MANE Select	c.844_846delGTTinsATC p.Val282Ile	missense	N/A	Prot: NP_064425.2
	SLC2A9 NM_001001290.2		c.757_759delGTTinsATC p.Val253Ile	missense	N/A	Prot: NP_001001290.1 UniProt:

SLC2A9 NM_020041.3

MANE Select

HGVSc / HGVSpc.844_846delGTTinsATCp.Val282Ile

Exon rankN/A

missense

Prot: NP_064425.2

SLC2A9 NM_001001290.2

HGVSc / HGVSpc.757_759delGTTinsATCp.Val253Ile

Exon rankN/A

missense

Prot: NP_001001290.1UniProt: Q9NRM0-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	SLC2A9 ENST00000264784.8	TSL:1MANE Select	c.844_846delGTTinsATC p.Val282Ile	missense	N/A	Prot: ENSP00000264784.3 UniProt:
	SLC2A9 ENST00000309065.7	TSL:1	c.757_759delGTTinsATC p.Val253Ile	missense	N/A	Prot: ENSP00000311383.3 UniProt:
	SLC2A9 ENST00000505104.5	TSL:1	n.878_880delGTTinsATC	non_coding_transcript_exon	Exon 8 of 12	Prot:

SLC2A9 ENST00000264784.8

TSL:1MANE Select

HGVSc / HGVSpc.844_846delGTTinsATCp.Val282Ile

Exon rankN/A

missense

Prot: ENSP00000264784.3UniProt: Q9NRM0-1

SLC2A9 ENST00000309065.7

TSL:1

HGVSc / HGVSpc.757_759delGTTinsATCp.Val253Ile

Exon rankN/A

missense

Prot: ENSP00000311383.3UniProt: Q9NRM0-2

SLC2A9 ENST00000505104.5

TSL:1

HGVSc / HGVSpn.878_880delGTTinsATC

Exon rankExon 8 of 12

non_coding_transcript_exon

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Uncertain	6.8

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

hg19: chr4-9922165;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar