chr1-42929016-T-C

Variant names:

• chr1-42929016-T-C
• NM_006516.4:c.990A>G
• SLC2A1 p.Arg330Arg

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-2 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB4_Strong

The NM_006516.4(SLC2A1):c.990A>G (p.Arg330Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The gene SLC2A1 is a tumor suppressor gene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). The gene SLC2A1 is a known oncogene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). The gene SLC2A1 is a cancer driver gene (CancerMine: 3 TSG, 14 oncogene, 1 driver citations). The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC2A1 NM_006516.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 0 publications found

Genes affected

SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]

SLC2A1 Gene-Disease associations (from GenCC):

• encephalopathy due to GLUT1 deficiency

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P
• GLUT1 deficiency syndrome

  Inheritance: SD, AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, ClinGen
• childhood onset GLUT1 deficiency syndrome 2

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
• dystonia 9

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet
• epilepsy, idiopathic generalized, susceptibility to, 12

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• childhood absence epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary cryohydrocytosis with reduced stomatin

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• myoclonic-astatic epilepsy

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -2 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])
	B4Synonymous/intronic, no splicing impact		Synonymous/intronic variant with confirmed no splicing impact (B4 strong); Synonymous variant — splicing algorithms confirm no impact on splicing (B4 strong [-4])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_006516.4. 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
	SLC2A1 NM_006516.4	MANE Select	c.990A>G p.Arg330Arg	synonymous	Exon 8 of 10	Prot: NP_006507.2 UniProt:

SLC2A1 NM_006516.4

MANE Select

HGVSc / HGVSpc.990A>Gp.Arg330Arg

Exon rankExon 8 of 10

synonymous

Prot: NP_006507.2UniProt: P11166

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	SLC2A1 ENST00000426263.10	TSL:1MANE Select	c.990A>G p.Arg330Arg	synonymous	Exon 8 of 10	Prot: ENSP00000416293.2 UniProt:
	SLC2A1 ENST00000889577.1		c.987A>G p.Arg329Arg	synonymous	Exon 8 of 10	Prot: ENSP00000559636.1 UniProt:
	SLC2A1 ENST00000958848.1		c.990A>G p.Arg330Arg	synonymous	Exon 8 of 10	Prot: ENSP00000628907.1 UniProt:

SLC2A1 ENST00000426263.10

TSL:1MANE Select

HGVSc / HGVSpc.990A>Gp.Arg330Arg

Exon rankExon 8 of 10

synonymous

Prot: ENSP00000416293.2UniProt: P11166

SLC2A1 ENST00000889577.1

HGVSc / HGVSpc.987A>Gp.Arg329Arg

Exon rankExon 8 of 10

synonymous

Prot: ENSP00000559636.1UniProt: A0ACI8RFT3

SLC2A1 ENST00000958848.1

HGVSc / HGVSpc.990A>Gp.Arg330Arg

Exon rankExon 8 of 10

synonymous

Prot: ENSP00000628907.1UniProt: A0ACI8V0G7

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 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Uncertain	11
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.70
GPN-Star LLR	N/A	-3.2
GPN-Star score	N/A	3.2
Mutation Taster	N/A	99/1	polymorphism
PhyloP100	Benign	-0.34

Showing 8 of 8 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.010
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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: chr1-43394687;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar