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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: 5-79077492-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=79077492&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BHMT2",
"hgnc_id": 1048,
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_017614.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DMGDH",
"hgnc_id": 24475,
"hgvs_c": "n.607-21584G>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000520388.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.7258,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.657465934753418,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 363,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2603,
"cdna_start": 62,
"cds_end": null,
"cds_length": 1092,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_017614.5",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000255192.8",
"protein_coding": true,
"protein_id": "NP_060084.2",
"strand": true,
"transcript": "NM_017614.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 363,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2603,
"cdna_start": 62,
"cds_end": null,
"cds_length": 1092,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000255192.8",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017614.5",
"protein_coding": true,
"protein_id": "ENSP00000255192.3",
"strand": true,
"transcript": "ENST00000255192.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 369,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2002,
"cdna_start": 62,
"cds_end": null,
"cds_length": 1110,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896185.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566244.1",
"strand": true,
"transcript": "ENST00000896185.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 360,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2663,
"cdna_start": 132,
"cds_end": null,
"cds_length": 1083,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896179.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566238.1",
"strand": true,
"transcript": "ENST00000896179.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 352,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1955,
"cdna_start": 66,
"cds_end": null,
"cds_length": 1059,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896183.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566242.1",
"strand": true,
"transcript": "ENST00000896183.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 302,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2438,
"cdna_start": 81,
"cds_end": null,
"cds_length": 909,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896181.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566240.1",
"strand": true,
"transcript": "ENST00000896181.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 299,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2411,
"cdna_start": 62,
"cds_end": null,
"cds_length": 900,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001178005.2",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001171476.1",
"strand": true,
"transcript": "NM_001178005.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 299,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1537,
"cdna_start": 62,
"cds_end": null,
"cds_length": 900,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000521567.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000430278.1",
"strand": true,
"transcript": "ENST00000521567.1",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1781,
"cdna_start": 60,
"cds_end": null,
"cds_length": 891,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896186.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566245.1",
"strand": true,
"transcript": "ENST00000896186.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 288,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2112,
"cdna_start": 62,
"cds_end": null,
"cds_length": 867,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896182.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566241.1",
"strand": true,
"transcript": "ENST00000896182.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 268,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2361,
"cdna_start": 107,
"cds_end": null,
"cds_length": 807,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896180.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566239.1",
"strand": true,
"transcript": "ENST00000896180.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 219,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": 193,
"cds_end": null,
"cds_length": 660,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896177.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566236.1",
"strand": true,
"transcript": "ENST00000896177.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 158,
"aa_ref": "R",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2106,
"cdna_start": 181,
"cds_end": null,
"cds_length": 477,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000896178.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.46C>A",
"hgvs_p": "p.Arg16Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566237.1",
"strand": true,
"transcript": "ENST00000896178.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 67,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 524,
"cdna_start": null,
"cds_end": null,
"cds_length": 205,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000518666.5",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.-135C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428640.1",
"strand": true,
"transcript": "ENST00000518666.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1759,
"cdna_start": null,
"cds_end": null,
"cds_length": 867,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000896184.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "c.34-3195C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566243.1",
"strand": true,
"transcript": "ENST00000896184.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 528,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000518758.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "n.61C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000518758.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 578,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000519743.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "n.46C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000430155.1",
"strand": true,
"transcript": "ENST00000519743.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 702,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000523472.1",
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"hgvs_c": "n.53C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000523472.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 661,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000520388.5",
"gene_hgnc_id": 24475,
"gene_symbol": "DMGDH",
"hgvs_c": "n.607-21584G>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000520388.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs751383805",
"effect": "missense_variant",
"frequency_reference_population": 6.8434093e-7,
"gene_hgnc_id": 1048,
"gene_symbol": "BHMT2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84341e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.718,
"pos": 79077492,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.227,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10000000149011612,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.1,
"transcript": "NM_017614.5"
}
]
}