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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: 5-36197555-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=36197555&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 36197555,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001085411.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1176T>C",
"hgvs_p": "p.Arg392Arg",
"transcript": "NM_001085411.3",
"protein_id": "NP_001078880.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 442,
"cds_start": 1176,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000381937.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001085411.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1176T>C",
"hgvs_p": "p.Arg392Arg",
"transcript": "ENST00000381937.9",
"protein_id": "ENSP00000371362.4",
"transcript_support_level": 2,
"aa_start": 392,
"aa_end": null,
"aa_length": 442,
"cds_start": 1176,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001085411.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381937.9"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.687T>C",
"hgvs_p": "p.Arg229Arg",
"transcript": "ENST00000282512.7",
"protein_id": "ENSP00000282512.3",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 279,
"cds_start": 687,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000282512.7"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.591T>C",
"hgvs_p": "p.Arg197Arg",
"transcript": "ENST00000617628.4",
"protein_id": "ENSP00000480506.1",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 247,
"cds_start": 591,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000617628.4"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "n.905T>C",
"hgvs_p": null,
"transcript": "ENST00000404560.7",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000404560.7"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "n.560T>C",
"hgvs_p": null,
"transcript": "ENST00000511613.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000511613.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1281T>C",
"hgvs_p": "p.Arg427Arg",
"transcript": "ENST00000948923.1",
"protein_id": "ENSP00000618982.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 477,
"cds_start": 1281,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948923.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1215T>C",
"hgvs_p": "p.Arg405Arg",
"transcript": "ENST00000948924.1",
"protein_id": "ENSP00000618983.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 455,
"cds_start": 1215,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948924.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1080T>C",
"hgvs_p": "p.Arg360Arg",
"transcript": "ENST00000514504.5",
"protein_id": "ENSP00000421029.1",
"transcript_support_level": 5,
"aa_start": 360,
"aa_end": null,
"aa_length": 410,
"cds_start": 1080,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514504.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Arg251Arg",
"transcript": "NM_001287341.2",
"protein_id": "NP_001274270.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 301,
"cds_start": 753,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287341.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Arg251Arg",
"transcript": "ENST00000506945.5",
"protein_id": "ENSP00000422250.1",
"transcript_support_level": 2,
"aa_start": 251,
"aa_end": null,
"aa_length": 301,
"cds_start": 753,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506945.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.687T>C",
"hgvs_p": "p.Arg229Arg",
"transcript": "NM_001287340.2",
"protein_id": "NP_001274269.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 279,
"cds_start": 687,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287340.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.687T>C",
"hgvs_p": "p.Arg229Arg",
"transcript": "NM_153013.5",
"protein_id": "NP_694558.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 279,
"cds_start": 687,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153013.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.687T>C",
"hgvs_p": "p.Arg229Arg",
"transcript": "ENST00000397338.5",
"protein_id": "ENSP00000380499.1",
"transcript_support_level": 2,
"aa_start": 229,
"aa_end": null,
"aa_length": 279,
"cds_start": 687,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397338.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.258T>C",
"hgvs_p": "p.Arg86Arg",
"transcript": "ENST00000502355.5",
"protein_id": "ENSP00000424166.1",
"transcript_support_level": 5,
"aa_start": 86,
"aa_end": null,
"aa_length": 136,
"cds_start": 258,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502355.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.1242T>C",
"hgvs_p": "p.Arg414Arg",
"transcript": "XM_005248241.5",
"protein_id": "XP_005248298.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 464,
"cds_start": 1242,
"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": "XM_005248241.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Arg251Arg",
"transcript": "XM_024454360.2",
"protein_id": "XP_024310128.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 301,
"cds_start": 753,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024454360.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.753T>C",
"hgvs_p": "p.Arg251Arg",
"transcript": "XM_047416705.1",
"protein_id": "XP_047272661.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 301,
"cds_start": 753,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416705.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "c.687T>C",
"hgvs_p": "p.Arg229Arg",
"transcript": "XM_047416706.1",
"protein_id": "XP_047272662.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 279,
"cds_start": 687,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416706.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"hgvs_c": "n.546T>C",
"hgvs_p": null,
"transcript": "ENST00000509225.1",
"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": "ENST00000509225.1"
}
],
"gene_symbol": "NADK2",
"gene_hgnc_id": 26404,
"dbsnp": "rs1023280001",
"frequency_reference_population": 0.000013153568,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131536,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.035999998450279236,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.036,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.368,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001085411.3",
"gene_symbol": "NADK2",
"hgnc_id": 26404,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1176T>C",
"hgvs_p": "p.Arg392Arg"
}
],
"clinvar_disease": "Progressive encephalopathy with leukodystrophy due to DECR deficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Progressive encephalopathy with leukodystrophy due to DECR deficiency",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}