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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: 1-31790892-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=31790892&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 31790892,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_144569.7",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3362A>G",
"hgvs_p": "p.Gln1121Arg",
"transcript": "NM_144569.7",
"protein_id": "NP_653170.3",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1216,
"cds_start": 3362,
"cds_end": null,
"cds_length": 3651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000360482.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144569.7"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3362A>G",
"hgvs_p": "p.Gln1121Arg",
"transcript": "ENST00000360482.7",
"protein_id": "ENSP00000353670.2",
"transcript_support_level": 2,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1216,
"cds_start": 3362,
"cds_end": null,
"cds_length": 3651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_144569.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360482.7"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3323A>G",
"hgvs_p": "p.Gln1108Arg",
"transcript": "NM_001281987.3",
"protein_id": "NP_001268916.1",
"transcript_support_level": null,
"aa_start": 1108,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3323,
"cds_end": null,
"cds_length": 3612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281987.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3323A>G",
"hgvs_p": "p.Gln1108Arg",
"transcript": "ENST00000533231.5",
"protein_id": "ENSP00000435851.1",
"transcript_support_level": 5,
"aa_start": 1108,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3323,
"cds_end": null,
"cds_length": 3612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000533231.5"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3320A>G",
"hgvs_p": "p.Gln1107Arg",
"transcript": "ENST00000917879.1",
"protein_id": "ENSP00000587938.1",
"transcript_support_level": null,
"aa_start": 1107,
"aa_end": null,
"aa_length": 1202,
"cds_start": 3320,
"cds_end": null,
"cds_length": 3609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917879.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3104A>G",
"hgvs_p": "p.Gln1035Arg",
"transcript": "ENST00000917880.1",
"protein_id": "ENSP00000587939.1",
"transcript_support_level": null,
"aa_start": 1035,
"aa_end": null,
"aa_length": 1130,
"cds_start": 3104,
"cds_end": null,
"cds_length": 3393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917880.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1802A>G",
"hgvs_p": "p.Gln601Arg",
"transcript": "NM_001281988.3",
"protein_id": "NP_001268917.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 696,
"cds_start": 1802,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281988.3"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1802A>G",
"hgvs_p": "p.Gln601Arg",
"transcript": "ENST00000257100.7",
"protein_id": "ENSP00000257100.3",
"transcript_support_level": 2,
"aa_start": 601,
"aa_end": null,
"aa_length": 696,
"cds_start": 1802,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000257100.7"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"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": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1631A>G",
"hgvs_p": "p.Gln544Arg",
"transcript": "ENST00000452755.6",
"protein_id": "ENSP00000399778.2",
"transcript_support_level": 5,
"aa_start": 544,
"aa_end": null,
"aa_length": 639,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1920,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452755.6"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"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": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1241A>G",
"hgvs_p": "p.Gln414Arg",
"transcript": "NM_001394397.1",
"protein_id": "NP_001381326.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 509,
"cds_start": 1241,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394397.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1115A>G",
"hgvs_p": "p.Gln372Arg",
"transcript": "NM_001394398.1",
"protein_id": "NP_001381327.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 467,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394398.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3320A>G",
"hgvs_p": "p.Gln1107Arg",
"transcript": "XM_017002779.2",
"protein_id": "XP_016858268.1",
"transcript_support_level": null,
"aa_start": 1107,
"aa_end": null,
"aa_length": 1202,
"cds_start": 3320,
"cds_end": null,
"cds_length": 3609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017002779.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3281A>G",
"hgvs_p": "p.Gln1094Arg",
"transcript": "XM_047433811.1",
"protein_id": "XP_047289767.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1189,
"cds_start": 3281,
"cds_end": null,
"cds_length": 3570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047433811.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.3197A>G",
"hgvs_p": "p.Gln1066Arg",
"transcript": "XM_017002781.2",
"protein_id": "XP_016858270.1",
"transcript_support_level": null,
"aa_start": 1066,
"aa_end": null,
"aa_length": 1161,
"cds_start": 3197,
"cds_end": null,
"cds_length": 3486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017002781.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.2552A>G",
"hgvs_p": "p.Gln851Arg",
"transcript": "XM_017002782.2",
"protein_id": "XP_016858271.1",
"transcript_support_level": null,
"aa_start": 851,
"aa_end": null,
"aa_length": 946,
"cds_start": 2552,
"cds_end": null,
"cds_length": 2841,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017002782.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.2426A>G",
"hgvs_p": "p.Gln809Arg",
"transcript": "XM_047433825.1",
"protein_id": "XP_047289781.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 904,
"cds_start": 2426,
"cds_end": null,
"cds_length": 2715,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047433825.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.1802A>G",
"hgvs_p": "p.Gln601Arg",
"transcript": "XM_011542413.3",
"protein_id": "XP_011540715.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 696,
"cds_start": 1802,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542413.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "c.*184A>G",
"hgvs_p": null,
"transcript": "NM_001394399.1",
"protein_id": "NP_001381328.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 289,
"cds_start": null,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394399.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"hgvs_c": "n.1474A>G",
"hgvs_p": null,
"transcript": "ENST00000473361.5",
"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": "ENST00000473361.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254545",
"gene_hgnc_id": null,
"hgvs_c": "n.356-249T>C",
"hgvs_p": null,
"transcript": "ENST00000527035.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000527035.1"
}
],
"gene_symbol": "SPOCD1",
"gene_hgnc_id": 26338,
"dbsnp": "rs1570140588",
"frequency_reference_population": 6.9856304e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.98563e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.041024982929229736,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.014,
"revel_prediction": "Benign",
"alphamissense_score": 0.0745,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.159,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_144569.7",
"gene_symbol": "SPOCD1",
"hgnc_id": 26338,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3362A>G",
"hgvs_p": "p.Gln1121Arg"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000527035.1",
"gene_symbol": "ENSG00000254545",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.356-249T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}