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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: 9-68783170-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=68783170&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 68783170,
"ref": "A",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000394264.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PABIR1",
"gene_hgnc_id": 23490,
"hgvs_c": "c.*2142A>T",
"hgvs_p": null,
"transcript": "NM_138333.5",
"protein_id": "NP_612206.5",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": -4,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5502,
"mane_select": "ENST00000394264.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PABIR1",
"gene_hgnc_id": 23490,
"hgvs_c": "c.*2142A>T",
"hgvs_p": null,
"transcript": "ENST00000394264.7",
"protein_id": "ENSP00000377807.5",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": -4,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5502,
"mane_select": "NM_138333.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_003558.4",
"protein_id": "NP_003549.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 540,
"cds_start": -4,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": "ENST00000265382.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "ENST00000265382.8",
"protein_id": "ENSP00000265382.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 540,
"cds_start": -4,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": "NM_003558.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "n.-85-35291A>T",
"hgvs_p": null,
"transcript": "ENST00000478500.3",
"protein_id": "ENSP00000435778.1",
"transcript_support_level": 1,
"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": 3335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001376036.1",
"protein_id": "NP_001362965.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 540,
"cds_start": -4,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001376037.1",
"protein_id": "NP_001362966.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 540,
"cds_start": -4,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001376039.1",
"protein_id": "NP_001362968.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 540,
"cds_start": -4,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001278253.2",
"protein_id": "NP_001265182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 502,
"cds_start": -4,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001376040.1",
"protein_id": "NP_001362969.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 502,
"cds_start": -4,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "NM_001376041.1",
"protein_id": "NP_001362970.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 502,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 14,
"intron_rank": 1,
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"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "ENST00000541509.5",
"protein_id": "ENSP00000438082.1",
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"aa_start": null,
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"aa_length": 502,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2664,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "ENST00000437200.5",
"protein_id": "ENSP00000398587.1",
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": 161,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 7,
"intron_rank": 2,
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"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
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"transcript": "ENST00000440050.5",
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},
{
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],
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"intron_rank": 2,
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"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "ENST00000377284.5",
"protein_id": "ENSP00000366498.1",
"transcript_support_level": 3,
"aa_start": null,
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"aa_length": 102,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": 4,
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"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "n.654-2913A>T",
"hgvs_p": null,
"transcript": "ENST00000472907.6",
"protein_id": null,
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},
{
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"consequences": [
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],
"exon_rank": null,
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"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "XM_005252262.6",
"protein_id": "XP_005252319.1",
"transcript_support_level": null,
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "XM_011519082.3",
"protein_id": "XP_011517384.1",
"transcript_support_level": null,
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"cds_start": -4,
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"mane_select": null,
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 2,
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"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-229-2913A>T",
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"transcript": "XM_011519084.4",
"protein_id": "XP_011517386.1",
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},
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],
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"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
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"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "XM_017015188.2",
"protein_id": "XP_016870677.1",
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},
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],
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"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 17,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-85-35291A>T",
"hgvs_p": null,
"transcript": "XM_047423951.1",
"protein_id": "XP_047279907.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 540,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3285,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIP5K1B",
"gene_hgnc_id": 8995,
"hgvs_c": "c.-229-2913A>T",
"hgvs_p": null,
"transcript": "XM_047423952.1",
"protein_id": "XP_047279908.1",
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"cds_start": -4,
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}
],
"gene_symbol": "PABIR1",
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"dbsnp": "rs12006032",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
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"gnomad_genomes_af": null,
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"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.266,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
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"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000394264.7",
"gene_symbol": "PABIR1",
"hgnc_id": 23490,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*2142A>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000478500.3",
"gene_symbol": "PIP5K1B",
"hgnc_id": 8995,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.-85-35291A>T",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}