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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: 19-12940316-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12940316&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12940316,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004343.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "NM_004343.4",
"protein_id": "NP_004334.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 417,
"cds_start": 566,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1901,
"mane_select": "ENST00000316448.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004343.4"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000316448.10",
"protein_id": "ENSP00000320866.4",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 417,
"cds_start": 566,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1901,
"mane_select": "NM_004343.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316448.10"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000957023.1",
"protein_id": "ENSP00000627082.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 415,
"cds_start": 566,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1895,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957023.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000929790.1",
"protein_id": "ENSP00000599849.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 413,
"cds_start": 566,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1889,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929790.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000929788.1",
"protein_id": "ENSP00000599847.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 410,
"cds_start": 566,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1880,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929788.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000929786.1",
"protein_id": "ENSP00000599845.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 387,
"cds_start": 566,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929786.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000586760.2",
"protein_id": "ENSP00000465918.2",
"transcript_support_level": 2,
"aa_start": 189,
"aa_end": null,
"aa_length": 378,
"cds_start": 566,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1630,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586760.2"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.362G>C",
"hgvs_p": "p.Ser121Thr",
"transcript": "ENST00000588454.6",
"protein_id": "ENSP00000465105.2",
"transcript_support_level": 3,
"aa_start": 121,
"aa_end": null,
"aa_length": 349,
"cds_start": 362,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 397,
"cdna_end": null,
"cdna_length": 1661,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588454.6"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr",
"transcript": "ENST00000929789.1",
"protein_id": "ENSP00000599848.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 311,
"cds_start": 566,
"cds_end": null,
"cds_length": 936,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 1583,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929789.1"
},
{
"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": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.430-56G>C",
"hgvs_p": null,
"transcript": "ENST00000929787.1",
"protein_id": "ENSP00000599846.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 353,
"cds_start": null,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1709,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929787.1"
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.549+17G>C",
"hgvs_p": null,
"transcript": "ENST00000929792.1",
"protein_id": "ENSP00000599851.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 264,
"cds_start": null,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1442,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929792.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.549+17G>C",
"hgvs_p": null,
"transcript": "ENST00000929791.1",
"protein_id": "ENSP00000599850.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 231,
"cds_start": null,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1343,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929791.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "c.45+1592G>C",
"hgvs_p": null,
"transcript": "ENST00000861560.1",
"protein_id": "ENSP00000531619.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": null,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 986,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861560.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "n.566G>C",
"hgvs_p": null,
"transcript": "ENST00000586967.2",
"protein_id": "ENSP00000466037.2",
"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": 1678,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000586967.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "n.727G>C",
"hgvs_p": null,
"transcript": "ENST00000590325.1",
"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": 781,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000590325.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "n.566G>C",
"hgvs_p": null,
"transcript": "ENST00000680816.1",
"protein_id": "ENSP00000504963.1",
"transcript_support_level": null,
"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": 1564,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680816.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6515",
"gene_hgnc_id": 50227,
"hgvs_c": "n.-168G>C",
"hgvs_p": null,
"transcript": "ENST00000619843.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 57,
"mane_select": null,
"mane_plus": null,
"biotype": "miRNA",
"feature": "ENST00000619843.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6515",
"gene_hgnc_id": 50227,
"hgvs_c": "n.-168G>C",
"hgvs_p": null,
"transcript": "NR_106770.1",
"protein_id": null,
"transcript_support_level": null,
"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": 57,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_106770.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6515",
"gene_hgnc_id": 50227,
"hgvs_c": "n.-170G>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_3232",
"protein_id": null,
"transcript_support_level": null,
"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": 21,
"mane_select": null,
"mane_plus": null,
"biotype": "miRNA",
"feature": "unassigned_transcript_3232"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6515",
"gene_hgnc_id": 50227,
"hgvs_c": "n.-205G>C",
"hgvs_p": null,
"transcript": "unassigned_transcript_3233",
"protein_id": null,
"transcript_support_level": null,
"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": 20,
"mane_select": null,
"mane_plus": null,
"biotype": "miRNA",
"feature": "unassigned_transcript_3233"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"hgvs_c": "n.*169G>C",
"hgvs_p": null,
"transcript": "ENST00000587486.6",
"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": 957,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000587486.6"
}
],
"gene_symbol": "CALR",
"gene_hgnc_id": 1455,
"dbsnp": "rs147369833",
"frequency_reference_population": 0.001509103,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2436,
"gnomad_exomes_af": 0.00157673,
"gnomad_genomes_af": 0.000860043,
"gnomad_exomes_ac": 2305,
"gnomad_genomes_ac": 131,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.022202253341674805,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.036,
"revel_prediction": "Benign",
"alphamissense_score": 0.0567,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.637,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004343.4",
"gene_symbol": "CALR",
"hgnc_id": 1455,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.566G>C",
"hgvs_p": "p.Ser189Thr"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NR_106770.1",
"gene_symbol": "MIR6515",
"hgnc_id": 50227,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-168G>C",
"hgvs_p": null
}
],
"clinvar_disease": "CALR-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "CALR-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}