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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: 2-197487080-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=197487080&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 197487080,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000388968.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "NM_002156.5",
"protein_id": "NP_002147.2",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1749,
"cdna_end": null,
"cdna_length": 2245,
"mane_select": "ENST00000388968.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000388968.8",
"protein_id": "ENSP00000373620.3",
"transcript_support_level": 1,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1749,
"cdna_end": null,
"cdna_length": 2245,
"mane_select": "NM_002156.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "NM_199440.2",
"protein_id": "NP_955472.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000345042.6",
"protein_id": "ENSP00000340019.2",
"transcript_support_level": 5,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 2299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000418022.2",
"protein_id": "ENSP00000412227.2",
"transcript_support_level": 4,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 2046,
"cdna_end": null,
"cdna_length": 2540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000426480.2",
"protein_id": "ENSP00000414446.2",
"transcript_support_level": 4,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1818,
"cdna_end": null,
"cdna_length": 2312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000428204.6",
"protein_id": "ENSP00000396460.2",
"transcript_support_level": 4,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1955,
"cdna_end": null,
"cdna_length": 2449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000439605.2",
"protein_id": "ENSP00000402478.2",
"transcript_support_level": 4,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 2016,
"cdna_end": null,
"cdna_length": 2510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000452200.6",
"protein_id": "ENSP00000412717.2",
"transcript_support_level": 5,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1913,
"cdna_end": null,
"cdna_length": 2407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000677913.1",
"protein_id": "ENSP00000503139.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1763,
"cdna_end": null,
"cdna_length": 2257,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala",
"transcript": "ENST00000678761.1",
"protein_id": "ENSP00000503894.1",
"transcript_support_level": null,
"aa_start": 563,
"aa_end": null,
"aa_length": 573,
"cds_start": 1688,
"cds_end": null,
"cds_length": 1722,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 2252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"transcript": "ENST00000676933.1",
"protein_id": "ENSP00000503144.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 541,
"cds_start": 1592,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 1706,
"cdna_end": null,
"cdna_length": 2200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.1415G>C",
"hgvs_p": "p.Gly472Ala",
"transcript": "ENST00000678170.1",
"protein_id": "ENSP00000503910.1",
"transcript_support_level": null,
"aa_start": 472,
"aa_end": null,
"aa_length": 482,
"cds_start": 1415,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 2022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*1494G>C",
"hgvs_p": null,
"transcript": "ENST00000440114.2",
"protein_id": "ENSP00000390404.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.4436G>C",
"hgvs_p": null,
"transcript": "ENST00000461097.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.2736G>C",
"hgvs_p": null,
"transcript": "ENST00000476746.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*684G>C",
"hgvs_p": null,
"transcript": "ENST00000677403.1",
"protein_id": "ENSP00000504667.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*857G>C",
"hgvs_p": null,
"transcript": "ENST00000677454.1",
"protein_id": "ENSP00000503295.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*697G>C",
"hgvs_p": null,
"transcript": "ENST00000677792.1",
"protein_id": "ENSP00000504645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 2195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*998G>C",
"hgvs_p": null,
"transcript": "ENST00000678545.1",
"protein_id": "ENSP00000502920.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.3278G>C",
"hgvs_p": null,
"transcript": "ENST00000678969.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "n.*697G>C",
"hgvs_p": null,
"transcript": "ENST00000679291.1",
"protein_id": "ENSP00000504417.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPD1",
"gene_hgnc_id": 5261,
"hgvs_c": "c.*166G>C",
"hgvs_p": null,
"transcript": "ENST00000678621.1",
"protein_id": "ENSP00000504328.1",
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},
{
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}
],
"gene_symbol": "HSPD1",
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"dbsnp": "rs41265953",
"frequency_reference_population": 0.019534314,
"hom_count_reference_population": 399,
"allele_count_reference_population": 29828,
"gnomad_exomes_af": 0.0199534,
"gnomad_genomes_af": 0.0157486,
"gnomad_exomes_ac": 27431,
"gnomad_genomes_ac": 2397,
"gnomad_exomes_homalt": 373,
"gnomad_genomes_homalt": 26,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008711159229278564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.55,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2447,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.979,
"phylop100way_prediction": "Uncertain_significance",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000388968.8",
"gene_symbol": "HSPD1",
"hgnc_id": 5261,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1688G>C",
"hgvs_p": "p.Gly563Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NR_132788.1",
"gene_symbol": "SNORA105B",
"hgnc_id": 51398,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-177G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 13,Spastic paraplegia,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Spastic paraplegia|Hereditary spastic paraplegia 13|not provided|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}