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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: 12-112419079-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112419079&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112419079,
"ref": "G",
"alt": "A",
"effect": "5_prime_UTR_variant",
"transcript": "NM_002834.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "NM_002834.5",
"protein_id": "NP_002825.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": -4,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6073,
"mane_select": "ENST00000351677.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000351677.7",
"protein_id": "ENSP00000340944.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": -4,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6073,
"mane_select": "NM_002834.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000392597.5",
"protein_id": "ENSP00000376376.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 460,
"cds_start": -4,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.571G>A",
"hgvs_p": null,
"transcript": "ENST00000531326.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000685487.1",
"protein_id": "ENSP00000508503.1",
"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": 6926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000692624.1",
"protein_id": "ENSP00000508953.1",
"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": 6045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000690210.1",
"protein_id": "ENSP00000509272.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 671,
"cds_start": -4,
"cds_end": null,
"cds_length": 2016,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "NM_001330437.2",
"protein_id": "NP_001317366.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 597,
"cds_start": -4,
"cds_end": null,
"cds_length": 1794,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "NM_001374625.1",
"protein_id": "NP_001361554.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 592,
"cds_start": -4,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000639857.2",
"protein_id": "ENSP00000491593.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000687906.1",
"protein_id": "ENSP00000509536.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 555,
"cds_start": -4,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000688597.1",
"protein_id": "ENSP00000510628.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 468,
"cds_start": -4,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
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"cdna_length": 5738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "NM_080601.3",
"protein_id": "NP_542168.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 460,
"cds_start": -4,
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"cds_length": 1383,
"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000685487.1",
"protein_id": "ENSP00000508503.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "n.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000692624.1",
"protein_id": "ENSP00000508953.1",
"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": 6045,
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "XM_011538613.3",
"protein_id": "XP_011536915.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"hgvs_c": "c.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000635625.1",
"protein_id": "ENSP00000489597.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 597,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL6",
"gene_hgnc_id": 10362,
"hgvs_c": "c.-580C>T",
"hgvs_p": null,
"transcript": "NM_001320141.2",
"protein_id": "NP_001307070.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
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"cdna_length": 1238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL6",
"gene_hgnc_id": 10362,
"hgvs_c": "c.-580C>T",
"hgvs_p": null,
"transcript": "ENST00000551291.6",
"protein_id": "ENSP00000448067.2",
"transcript_support_level": 3,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 700,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL6",
"gene_hgnc_id": 10362,
"hgvs_c": "c.-682C>T",
"hgvs_p": null,
"transcript": "XM_047429302.1",
"protein_id": "XP_047285258.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL6",
"gene_hgnc_id": 10362,
"hgvs_c": "c.-576C>T",
"hgvs_p": null,
"transcript": "XM_047429303.1",
"protein_id": "XP_047285259.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL6",
"gene_hgnc_id": 10362,
"hgvs_c": "c.-676C>T",
"hgvs_p": null,
"transcript": "XM_047429304.1",
"protein_id": "XP_047285260.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN11",
"gene_hgnc_id": 9644,
"dbsnp": "rs2135817333",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.38999998569488525,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.5600000023841858,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.139,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.56,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,BP6_Moderate",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002834.5",
"gene_symbol": "PTPN11",
"hgnc_id": 9644,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-33G>A",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001320141.2",
"gene_symbol": "RPL6",
"hgnc_id": 10362,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-580C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}