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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: 6-63684369-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=63684369&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 63684369,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000262043.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "NM_001370348.2",
"protein_id": "NP_001357277.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 2039,
"cds_start": 647,
"cds_end": null,
"cds_length": 6120,
"cdna_start": 1021,
"cdna_end": null,
"cdna_length": 18797,
"mane_select": "ENST00000262043.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "ENST00000262043.8",
"protein_id": "ENSP00000262043.4",
"transcript_support_level": 5,
"aa_start": 216,
"aa_end": null,
"aa_length": 2039,
"cds_start": 647,
"cds_end": null,
"cds_length": 6120,
"cdna_start": 1021,
"cdna_end": null,
"cdna_length": 18797,
"mane_select": "NM_001370348.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "ENST00000393387.5",
"protein_id": "ENSP00000377048.1",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 2039,
"cds_start": 647,
"cds_end": null,
"cds_length": 6120,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 6947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ser30Phe",
"transcript": "ENST00000506783.5",
"protein_id": "ENSP00000424694.1",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 1071,
"cds_start": 89,
"cds_end": null,
"cds_length": 3217,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "ENST00000509330.5",
"protein_id": "ENSP00000422841.1",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 736,
"cds_start": 647,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 1014,
"cdna_end": null,
"cdna_length": 2969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "n.*591C>T",
"hgvs_p": null,
"transcript": "ENST00000509876.5",
"protein_id": "ENSP00000424994.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "n.*591C>T",
"hgvs_p": null,
"transcript": "ENST00000509876.5",
"protein_id": "ENSP00000424994.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "NM_015153.4",
"protein_id": "NP_055968.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 2039,
"cds_start": 647,
"cds_end": null,
"cds_length": 6120,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 18449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "NM_001290259.2",
"protein_id": "NP_001277188.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 1951,
"cds_start": 383,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1214,
"cdna_end": null,
"cdna_length": 18990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "NM_001370349.2",
"protein_id": "NP_001357278.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 1951,
"cds_start": 383,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 18528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.506C>T",
"hgvs_p": "p.Ser169Phe",
"transcript": "ENST00000494284.6",
"protein_id": "ENSP00000424078.1",
"transcript_support_level": 2,
"aa_start": 169,
"aa_end": null,
"aa_length": 820,
"cds_start": 506,
"cds_end": null,
"cds_length": 2465,
"cdna_start": 895,
"cdna_end": null,
"cdna_length": 2854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "ENST00000481385.6",
"protein_id": "ENSP00000425227.1",
"transcript_support_level": 2,
"aa_start": 128,
"aa_end": null,
"aa_length": 812,
"cds_start": 383,
"cds_end": null,
"cds_length": 2439,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 2787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe",
"transcript": "NM_001290260.2",
"protein_id": "NP_001277189.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 736,
"cds_start": 647,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 1014,
"cdna_end": null,
"cdna_length": 2969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.674C>T",
"hgvs_p": "p.Ser225Phe",
"transcript": "XM_011535648.4",
"protein_id": "XP_011533950.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 2048,
"cds_start": 674,
"cds_end": null,
"cds_length": 6147,
"cdna_start": 1365,
"cdna_end": null,
"cdna_length": 19141,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "XM_047418528.1",
"protein_id": "XP_047274484.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 1951,
"cds_start": 383,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 19011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "XM_047418529.1",
"protein_id": "XP_047274485.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 1951,
"cds_start": 383,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 938,
"cdna_end": null,
"cdna_length": 18714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.383C>T",
"hgvs_p": "p.Ser128Phe",
"transcript": "XM_047418530.1",
"protein_id": "XP_047274486.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 1951,
"cds_start": 383,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 866,
"cdna_end": null,
"cdna_length": 18642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.-5+4208C>T",
"hgvs_p": null,
"transcript": "NM_001370350.2",
"protein_id": "NP_001357279.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1308,
"cds_start": -4,
"cds_end": null,
"cds_length": 3927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 17014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.-5+4208C>T",
"hgvs_p": null,
"transcript": "ENST00000515594.5",
"protein_id": "ENSP00000425338.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 859,
"cds_start": -4,
"cds_end": null,
"cds_length": 2582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*124C>T",
"hgvs_p": null,
"transcript": "ENST00000514822.1",
"protein_id": "ENSP00000424197.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": -4,
"cds_end": null,
"cds_length": 313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"dbsnp": "rs1357540567",
"frequency_reference_population": 0.000013145441,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131454,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22440633177757263,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.101,
"revel_prediction": "Benign",
"alphamissense_score": 0.1444,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.487,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000262043.8",
"gene_symbol": "PHF3",
"hgnc_id": 8921,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Phe"
}
],
"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
}