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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-42928941-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=42928941&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 42928941,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_006516.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1065A>G",
"hgvs_p": "p.Leu355Leu",
"transcript": "NM_006516.4",
"protein_id": "NP_006507.2",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 492,
"cds_start": 1065,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000426263.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006516.4"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1065A>G",
"hgvs_p": "p.Leu355Leu",
"transcript": "ENST00000426263.10",
"protein_id": "ENSP00000416293.2",
"transcript_support_level": 1,
"aa_start": 355,
"aa_end": null,
"aa_length": 492,
"cds_start": 1065,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006516.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426263.10"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1062A>G",
"hgvs_p": "p.Leu354Leu",
"transcript": "ENST00000889577.1",
"protein_id": "ENSP00000559636.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 491,
"cds_start": 1062,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889577.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1065A>G",
"hgvs_p": "p.Leu355Leu",
"transcript": "ENST00000958848.1",
"protein_id": "ENSP00000628907.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 491,
"cds_start": 1065,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958848.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1032A>G",
"hgvs_p": "p.Leu344Leu",
"transcript": "ENST00000938862.1",
"protein_id": "ENSP00000608921.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 481,
"cds_start": 1032,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938862.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.981A>G",
"hgvs_p": "p.Leu327Leu",
"transcript": "ENST00000938861.1",
"protein_id": "ENSP00000608920.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 464,
"cds_start": 981,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938861.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.663A>G",
"hgvs_p": "p.Leu221Leu",
"transcript": "ENST00000889576.1",
"protein_id": "ENSP00000559635.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 358,
"cds_start": 663,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889576.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.972+269A>G",
"hgvs_p": null,
"transcript": "ENST00000938860.1",
"protein_id": "ENSP00000608919.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 458,
"cds_start": null,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938860.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.1029+36A>G",
"hgvs_p": null,
"transcript": "ENST00000674765.1",
"protein_id": "ENSP00000501811.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 359,
"cds_start": null,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674765.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.867+652A>G",
"hgvs_p": null,
"transcript": "ENST00000958849.1",
"protein_id": "ENSP00000628908.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 355,
"cds_start": null,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958849.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.414+1685A>G",
"hgvs_p": null,
"transcript": "ENST00000475162.3",
"protein_id": "ENSP00000487213.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": null,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475162.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.*380A>G",
"hgvs_p": null,
"transcript": "ENST00000630287.2",
"protein_id": "ENSP00000486694.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000630287.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.559A>G",
"hgvs_p": null,
"transcript": "ENST00000674545.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000674545.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.1366A>G",
"hgvs_p": null,
"transcript": "ENST00000675112.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000675112.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.1514A>G",
"hgvs_p": null,
"transcript": "ENST00000676254.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000676254.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.*380A>G",
"hgvs_p": null,
"transcript": "ENST00000630287.2",
"protein_id": "ENSP00000486694.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000630287.2"
}
],
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"dbsnp": "rs2228490",
"frequency_reference_population": 0.008945856,
"hom_count_reference_population": 879,
"allele_count_reference_population": 14436,
"gnomad_exomes_af": 0.00544963,
"gnomad_genomes_af": 0.0424884,
"gnomad_exomes_ac": 7964,
"gnomad_genomes_ac": 6472,
"gnomad_exomes_homalt": 423,
"gnomad_genomes_homalt": 456,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6899999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.514,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_006516.4",
"gene_symbol": "SLC2A1",
"hgnc_id": 11005,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,SD,AD,Unknown",
"hgvs_c": "c.1065A>G",
"hgvs_p": "p.Leu355Leu"
}
],
"clinvar_disease": " 12, autosomal recessive, idiopathic generalized, susceptibility to,Childhood onset GLUT1 deficiency syndrome 2,Dystonia 9,Encephalopathy due to GLUT1 deficiency,Epilepsy,GLUT1 deficiency syndrome 1,Hereditary cryohydrocytosis with reduced stomatin,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:14",
"phenotype_combined": "not specified|Encephalopathy due to GLUT1 deficiency|GLUT1 deficiency syndrome 1, autosomal recessive|Dystonia 9|not provided|Inborn genetic diseases|Childhood onset GLUT1 deficiency syndrome 2|Hereditary cryohydrocytosis with reduced stomatin|Epilepsy, idiopathic generalized, susceptibility to, 12",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}