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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: 1-156876505-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=156876505&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM1",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NTRK1",
"hgnc_id": 8031,
"hgvs_c": "c.1738A>T",
"hgvs_p": "p.Thr580Ser",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_002529.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,BP4",
"acmg_score": 1,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.1526,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Hereditary insensitivity to pain with anhidrosis",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.408577561378479,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 796,
"aa_ref": "T",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2669,
"cdna_start": 1808,
"cds_end": null,
"cds_length": 2391,
"cds_start": 1738,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_002529.4",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1738A>T",
"hgvs_p": "p.Thr580Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000524377.7",
"protein_coding": true,
"protein_id": "NP_002520.2",
"strand": true,
"transcript": "NM_002529.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 796,
"aa_ref": "T",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2669,
"cdna_start": 1808,
"cds_end": null,
"cds_length": 2391,
"cds_start": 1738,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000524377.7",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1738A>T",
"hgvs_p": "p.Thr580Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002529.4",
"protein_coding": true,
"protein_id": "ENSP00000431418.1",
"strand": true,
"transcript": "ENST00000524377.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 790,
"aa_ref": "T",
"aa_start": 574,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2701,
"cdna_start": 1840,
"cds_end": null,
"cds_length": 2373,
"cds_start": 1720,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000368196.7",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1720A>T",
"hgvs_p": "p.Thr574Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000357179.3",
"strand": true,
"transcript": "ENST00000368196.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 793,
"aa_ref": "T",
"aa_start": 577,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2492,
"cdna_start": 1770,
"cds_end": null,
"cds_length": 2382,
"cds_start": 1729,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000358660.3",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1729A>T",
"hgvs_p": "p.Thr577Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000351486.3",
"strand": true,
"transcript": "ENST00000358660.3",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 790,
"aa_ref": "T",
"aa_start": 574,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": 1790,
"cds_end": null,
"cds_length": 2373,
"cds_start": 1720,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001012331.2",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1720A>T",
"hgvs_p": "p.Thr574Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001012331.1",
"strand": true,
"transcript": "NM_001012331.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 760,
"aa_ref": "T",
"aa_start": 544,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2571,
"cdna_start": 1710,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1630,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001007792.1",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1630A>T",
"hgvs_p": "p.Thr544Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001007793.1",
"strand": true,
"transcript": "NM_001007792.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 736,
"aa_ref": "T",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2665,
"cdna_start": 1804,
"cds_end": null,
"cds_length": 2211,
"cds_start": 1558,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000392302.7",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1558A>T",
"hgvs_p": "p.Thr520Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376120.3",
"strand": true,
"transcript": "ENST00000392302.7",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 736,
"aa_ref": "T",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2825,
"cdna_start": 1964,
"cds_end": null,
"cds_length": 2211,
"cds_start": 1558,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000674537.2",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1558A>T",
"hgvs_p": "p.Thr520Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502725.1",
"strand": true,
"transcript": "ENST00000674537.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2248,
"cdna_start": 1387,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1309,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000956587.1",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "c.1309A>T",
"hgvs_p": "p.Thr437Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626646.1",
"strand": true,
"transcript": "ENST00000956587.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2508,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000497019.7",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "n.*330A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000436804.2",
"strand": true,
"transcript": "ENST00000497019.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3052,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000530298.5",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "n.2191A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000530298.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2508,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000497019.7",
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"hgvs_c": "n.*330A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000436804.2",
"strand": true,
"transcript": "ENST00000497019.7",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs764541952",
"effect": "missense_variant",
"frequency_reference_population": 0.00000410568,
"gene_hgnc_id": 8031,
"gene_symbol": "NTRK1",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000410568,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Hereditary insensitivity to pain with anhidrosis",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.215,
"pos": 156876505,
"ref": "A",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.503,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002529.4"
}
]
}