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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: 2-42704285-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=42704285&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 42704285,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001330442.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1117C>T",
"hgvs_p": "p.Pro373Ser",
"transcript": "NM_001330442.2",
"protein_id": "NP_001317371.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 594,
"cds_start": 1117,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000405094.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330442.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1117C>T",
"hgvs_p": "p.Pro373Ser",
"transcript": "ENST00000405094.2",
"protein_id": "ENSP00000385823.1",
"transcript_support_level": 5,
"aa_start": 373,
"aa_end": null,
"aa_length": 594,
"cds_start": 1117,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001330442.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000405094.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Pro316Ser",
"transcript": "ENST00000406652.5",
"protein_id": "ENSP00000384249.1",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 537,
"cds_start": 946,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000406652.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1117C>T",
"hgvs_p": "p.Pro373Ser",
"transcript": "ENST00000407270.7",
"protein_id": "ENSP00000385045.3",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 515,
"cds_start": 1117,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000407270.7"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1114C>T",
"hgvs_p": "p.Pro372Ser",
"transcript": "NM_001330443.2",
"protein_id": "NP_001317372.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 593,
"cds_start": 1114,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330443.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1111C>T",
"hgvs_p": "p.Pro371Ser",
"transcript": "ENST00000956432.1",
"protein_id": "ENSP00000626491.1",
"transcript_support_level": null,
"aa_start": 371,
"aa_end": null,
"aa_length": 592,
"cds_start": 1111,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956432.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.952C>T",
"hgvs_p": "p.Pro318Ser",
"transcript": "ENST00000925935.1",
"protein_id": "ENSP00000595994.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 539,
"cds_start": 952,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925935.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Pro316Ser",
"transcript": "NM_001282755.2",
"protein_id": "NP_001269684.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 537,
"cds_start": 946,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282755.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Pro316Ser",
"transcript": "NM_001282756.2",
"protein_id": "NP_001269685.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 537,
"cds_start": 946,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282756.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.946C>T",
"hgvs_p": "p.Pro316Ser",
"transcript": "ENST00000405592.5",
"protein_id": "ENSP00000383973.1",
"transcript_support_level": 2,
"aa_start": 316,
"aa_end": null,
"aa_length": 537,
"cds_start": 946,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000405592.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.928C>T",
"hgvs_p": "p.Pro310Ser",
"transcript": "ENST00000860174.1",
"protein_id": "ENSP00000530233.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 531,
"cds_start": 928,
"cds_end": null,
"cds_length": 1596,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860174.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.925C>T",
"hgvs_p": "p.Pro309Ser",
"transcript": "NM_001330444.2",
"protein_id": "NP_001317373.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 530,
"cds_start": 925,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330444.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.925C>T",
"hgvs_p": "p.Pro309Ser",
"transcript": "ENST00000956431.1",
"protein_id": "ENSP00000626490.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 530,
"cds_start": 925,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956431.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1117C>T",
"hgvs_p": "p.Pro373Ser",
"transcript": "NM_020744.4",
"protein_id": "NP_065795.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 515,
"cds_start": 1117,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020744.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "c.1114C>T",
"hgvs_p": "p.Pro372Ser",
"transcript": "ENST00000406911.5",
"protein_id": "ENSP00000385241.1",
"transcript_support_level": 5,
"aa_start": 372,
"aa_end": null,
"aa_length": 514,
"cds_start": 1114,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000406911.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.1114C>T",
"hgvs_p": null,
"transcript": "ENST00000409019.5",
"protein_id": "ENSP00000386763.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000409019.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.1114C>T",
"hgvs_p": null,
"transcript": "ENST00000454356.5",
"protein_id": "ENSP00000391455.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000454356.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.637C>T",
"hgvs_p": null,
"transcript": "ENST00000467925.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000467925.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.303C>T",
"hgvs_p": null,
"transcript": "ENST00000472767.5",
"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": "pseudogene",
"feature": "ENST00000472767.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.1979C>T",
"hgvs_p": null,
"transcript": "ENST00000482875.5",
"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": "ENST00000482875.5"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"hgvs_c": "n.135-3618C>T",
"hgvs_p": null,
"transcript": "ENST00000475383.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000475383.5"
}
],
"gene_symbol": "MTA3",
"gene_hgnc_id": 23784,
"dbsnp": "rs775403666",
"frequency_reference_population": 0.0000061960404,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000478915,
"gnomad_genomes_af": 0.0000196985,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01793655753135681,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.009,
"revel_prediction": "Benign",
"alphamissense_score": 0.0625,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.407,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 8,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001330442.2",
"gene_symbol": "MTA3",
"hgnc_id": 23784,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1117C>T",
"hgvs_p": "p.Pro373Ser"
}
],
"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
}