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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: 19-47479889-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=47479889&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 47479889,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_007059.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.761T>C",
"hgvs_p": "p.Ile254Thr",
"transcript": "NM_007059.4",
"protein_id": "NP_008990.2",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 436,
"cds_start": 761,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000338134.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007059.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.761T>C",
"hgvs_p": "p.Ile254Thr",
"transcript": "ENST00000338134.8",
"protein_id": "ENSP00000337850.2",
"transcript_support_level": 1,
"aa_start": 254,
"aa_end": null,
"aa_length": 436,
"cds_start": 761,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007059.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338134.8"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.761T>C",
"hgvs_p": "p.Ile254Thr",
"transcript": "ENST00000914957.1",
"protein_id": "ENSP00000585016.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 474,
"cds_start": 761,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914957.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.593T>C",
"hgvs_p": "p.Ile198Thr",
"transcript": "ENST00000968682.1",
"protein_id": "ENSP00000638741.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 417,
"cds_start": 593,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968682.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.593T>C",
"hgvs_p": "p.Ile198Thr",
"transcript": "NM_001291296.2",
"protein_id": "NP_001278225.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 380,
"cds_start": 593,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291296.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.593T>C",
"hgvs_p": "p.Ile198Thr",
"transcript": "ENST00000595554.1",
"protein_id": "ENSP00000469446.1",
"transcript_support_level": 3,
"aa_start": 198,
"aa_end": null,
"aa_length": 262,
"cds_start": 593,
"cds_end": null,
"cds_length": 790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595554.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.41T>C",
"hgvs_p": "p.Ile14Thr",
"transcript": "ENST00000600271.5",
"protein_id": "ENSP00000472291.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 41,
"cds_start": 41,
"cds_end": null,
"cds_length": 128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600271.5"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.1013T>C",
"hgvs_p": "p.Ile338Thr",
"transcript": "XM_017026227.2",
"protein_id": "XP_016881716.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 559,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026227.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.1013T>C",
"hgvs_p": "p.Ile338Thr",
"transcript": "XM_017026228.2",
"protein_id": "XP_016881717.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 520,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026228.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.761T>C",
"hgvs_p": "p.Ile254Thr",
"transcript": "XM_024451333.2",
"protein_id": "XP_024307101.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 475,
"cds_start": 761,
"cds_end": null,
"cds_length": 1428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451333.2"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "c.732T>C",
"hgvs_p": "p.Asp244Asp",
"transcript": "ENST00000914958.1",
"protein_id": "ENSP00000585017.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 401,
"cds_start": 732,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914958.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "n.*395T>C",
"hgvs_p": null,
"transcript": "ENST00000594208.5",
"protein_id": "ENSP00000470364.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000594208.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "n.907T>C",
"hgvs_p": null,
"transcript": "NR_111923.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_111923.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"hgvs_c": "n.*395T>C",
"hgvs_p": null,
"transcript": "ENST00000594208.5",
"protein_id": "ENSP00000470364.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000594208.5"
}
],
"gene_symbol": "KPTN",
"gene_hgnc_id": 6404,
"dbsnp": "rs200513352",
"frequency_reference_population": 0.00042454185,
"hom_count_reference_population": 2,
"allele_count_reference_population": 685,
"gnomad_exomes_af": 0.000374973,
"gnomad_genomes_af": 0.000900936,
"gnomad_exomes_ac": 548,
"gnomad_genomes_ac": 137,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.012604176998138428,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.076,
"revel_prediction": "Benign",
"alphamissense_score": 0.0953,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.536,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_007059.4",
"gene_symbol": "KPTN",
"hgnc_id": 6404,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.761T>C",
"hgvs_p": "p.Ile254Thr"
}
],
"clinvar_disease": "Inborn genetic diseases,Macrocephaly-developmental delay syndrome,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Macrocephaly-developmental delay syndrome|not specified|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}