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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: 2-84433390-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=84433390&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 84433390,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003849.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "NM_003849.4",
"protein_id": "NP_003840.2",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 346,
"cds_start": 635,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393868.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003849.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "ENST00000393868.7",
"protein_id": "ENSP00000377446.2",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 346,
"cds_start": 635,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003849.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393868.7"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.662A>G",
"hgvs_p": "p.Gln221Arg",
"transcript": "ENST00000949558.1",
"protein_id": "ENSP00000619617.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 355,
"cds_start": 662,
"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": "ENST00000949558.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "ENST00000912793.1",
"protein_id": "ENSP00000582852.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 341,
"cds_start": 635,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912793.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "ENST00000900284.1",
"protein_id": "ENSP00000570343.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 332,
"cds_start": 635,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900284.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "ENST00000912791.1",
"protein_id": "ENSP00000582850.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 321,
"cds_start": 635,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912791.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.518A>G",
"hgvs_p": "p.Gln173Arg",
"transcript": "ENST00000912792.1",
"protein_id": "ENSP00000582851.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 307,
"cds_start": 518,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912792.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg",
"transcript": "ENST00000900285.1",
"protein_id": "ENSP00000570344.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 283,
"cds_start": 635,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900285.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.143A>G",
"hgvs_p": "p.Gln48Arg",
"transcript": "ENST00000912790.1",
"protein_id": "ENSP00000582849.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 182,
"cds_start": 143,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912790.1"
},
{
"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": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "c.590-1731A>G",
"hgvs_p": null,
"transcript": "ENST00000949559.1",
"protein_id": "ENSP00000619618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 318,
"cds_start": null,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949559.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "n.382A>G",
"hgvs_p": null,
"transcript": "ENST00000487809.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000487809.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "n.92A>G",
"hgvs_p": null,
"transcript": "ENST00000488234.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000488234.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "n.*75A>G",
"hgvs_p": null,
"transcript": "ENST00000651342.1",
"protein_id": "ENSP00000498471.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000651342.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"hgvs_c": "n.*75A>G",
"hgvs_p": null,
"transcript": "ENST00000651342.1",
"protein_id": "ENSP00000498471.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000651342.1"
}
],
"gene_symbol": "SUCLG1",
"gene_hgnc_id": 11449,
"dbsnp": "rs767781003",
"frequency_reference_population": 0.000012392679,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.00000410501,
"gnomad_genomes_af": 0.0000919685,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8808572292327881,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.897,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9752,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.13,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003849.4",
"gene_symbol": "SUCLG1",
"hgnc_id": 11449,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.635A>G",
"hgvs_p": "p.Gln212Arg"
}
],
"clinvar_disease": "Mitochondrial DNA depletion syndrome 9",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Mitochondrial DNA depletion syndrome 9",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}