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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: 20-35870979-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=35870979&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PHF20",
"hgnc_id": 16098,
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_016436.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_score": -8,
"allele_count_reference_population": 9,
"alphamissense_prediction": null,
"alphamissense_score": 0.0673,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "20",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.03745359182357788,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5879,
"cdna_start": 1044,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_016436.5",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374012.8",
"protein_coding": true,
"protein_id": "NP_057520.2",
"strand": true,
"transcript": "NM_016436.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5879,
"cdna_start": 1044,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000374012.8",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_016436.5",
"protein_coding": true,
"protein_id": "ENSP00000363124.3",
"strand": true,
"transcript": "ENST00000374012.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 548,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1814,
"cdna_start": 1113,
"cds_end": null,
"cds_length": 1648,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000374000.8",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363112.4",
"strand": true,
"transcript": "ENST00000374000.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1635,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000481202.5",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "n.953C>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": "ENST00000481202.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 609,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6697,
"cdna_start": null,
"cds_end": null,
"cds_length": 1830,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 15,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_005260421.4",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.-263C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005260478.1",
"strand": true,
"transcript": "XM_005260421.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 609,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5506,
"cdna_start": null,
"cds_end": null,
"cds_length": 1830,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 15,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011528844.3",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.-263C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527146.1",
"strand": true,
"transcript": "XM_011528844.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 609,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5886,
"cdna_start": null,
"cds_end": null,
"cds_length": 1830,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 18,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047440184.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.-263C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296140.1",
"strand": true,
"transcript": "XM_047440184.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 609,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5461,
"cdna_start": null,
"cds_end": null,
"cds_length": 1830,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 15,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047440185.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.-263C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296141.1",
"strand": true,
"transcript": "XM_047440185.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 609,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6309,
"cdna_start": null,
"cds_end": null,
"cds_length": 1830,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047440186.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.-263C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296142.1",
"strand": true,
"transcript": "XM_047440186.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1021,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5670,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 3066,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000937490.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607549.1",
"strand": true,
"transcript": "ENST00000937490.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6001,
"cdna_start": 1166,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000937489.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607548.1",
"strand": true,
"transcript": "ENST00000937489.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5687,
"cdna_start": 1138,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000937491.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607550.1",
"strand": true,
"transcript": "ENST00000937491.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 957,
"aa_ref": "S",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5739,
"cdna_start": 904,
"cds_end": null,
"cds_length": 2874,
"cds_start": 782,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000937487.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.782C>T",
"hgvs_p": "p.Ser261Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607546.1",
"strand": true,
"transcript": "ENST00000937487.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 919,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5647,
"cdna_start": 1091,
"cds_end": null,
"cds_length": 2760,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000937485.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607544.1",
"strand": true,
"transcript": "ENST00000937485.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 919,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3640,
"cdna_start": 1047,
"cds_end": null,
"cds_length": 2760,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000942256.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612315.1",
"strand": true,
"transcript": "ENST00000942256.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 856,
"aa_ref": "S",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5425,
"cdna_start": 590,
"cds_end": null,
"cds_length": 2571,
"cds_start": 479,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000937488.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.479C>T",
"hgvs_p": "p.Ser160Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607547.1",
"strand": true,
"transcript": "ENST00000937488.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 542,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1997,
"cdna_start": 1315,
"cds_end": null,
"cds_length": 1629,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000339089.10",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000341900.6",
"strand": true,
"transcript": "ENST00000339089.10",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5959,
"cdna_start": 1124,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047440180.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296136.1",
"strand": true,
"transcript": "XM_047440180.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6118,
"cdna_start": 1283,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047440181.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296137.1",
"strand": true,
"transcript": "XM_047440181.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "S",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6176,
"cdna_start": 1341,
"cds_end": null,
"cds_length": 3039,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047440182.1",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.947C>T",
"hgvs_p": "p.Ser316Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296138.1",
"strand": true,
"transcript": "XM_047440182.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 957,
"aa_ref": "S",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5714,
"cdna_start": 879,
"cds_end": null,
"cds_length": 2874,
"cds_start": 782,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_017027868.3",
"gene_hgnc_id": 16098,
"gene_symbol": "PHF20",
"hgvs_c": "c.782C>T",
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