← Back to variant description
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: 3-52421657-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52421657&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52421657,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016483.7",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "NM_016483.7",
"protein_id": "NP_057567.3",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000327906.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016483.7"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000327906.8",
"protein_id": "ENSP00000333024.3",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016483.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000327906.8"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000614886.4",
"protein_id": "ENSP00000480003.1",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 342,
"cds_start": 583,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614886.4"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "n.310C>T",
"hgvs_p": null,
"transcript": "ENST00000498509.2",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000498509.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "NM_001321126.2",
"protein_id": "NP_001308055.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321126.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "NM_001321127.2",
"protein_id": "NP_001308056.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321127.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000894733.1",
"protein_id": "ENSP00000564792.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894733.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "NM_001278221.3",
"protein_id": "NP_001265150.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 342,
"cds_start": 583,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278221.3"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000347025.6",
"protein_id": "ENSP00000246282.4",
"transcript_support_level": 5,
"aa_start": 195,
"aa_end": null,
"aa_length": 342,
"cds_start": 583,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347025.6"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000958980.1",
"protein_id": "ENSP00000629039.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 342,
"cds_start": 583,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958980.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000894735.1",
"protein_id": "ENSP00000564794.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 327,
"cds_start": 583,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894735.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.460C>T",
"hgvs_p": "p.His154Tyr",
"transcript": "ENST00000461861.5",
"protein_id": "ENSP00000417712.1",
"transcript_support_level": 5,
"aa_start": 154,
"aa_end": null,
"aa_length": 325,
"cds_start": 460,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000461861.5"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "ENST00000940047.1",
"protein_id": "ENSP00000610106.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 319,
"cds_start": 583,
"cds_end": null,
"cds_length": 960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940047.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.His161Tyr",
"transcript": "ENST00000894734.1",
"protein_id": "ENSP00000564793.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 308,
"cds_start": 481,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894734.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.His100Tyr",
"transcript": "ENST00000958981.1",
"protein_id": "ENSP00000629040.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 286,
"cds_start": 298,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958981.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.79C>T",
"hgvs_p": "p.His27Tyr",
"transcript": "ENST00000465863.1",
"protein_id": "ENSP00000420521.1",
"transcript_support_level": 3,
"aa_start": 27,
"aa_end": null,
"aa_length": 62,
"cds_start": 79,
"cds_end": null,
"cds_length": 189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000465863.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "XM_024453589.2",
"protein_id": "XP_024309357.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 381,
"cds_start": 583,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453589.2"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "XM_047448295.1",
"protein_id": "XP_047304251.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 342,
"cds_start": 583,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448295.1"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "XM_011533826.4",
"protein_id": "XP_011532128.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 269,
"cds_start": 583,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533826.4"
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr",
"transcript": "XM_047448296.1",
"protein_id": "XP_047304252.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 269,
"cds_start": 583,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448296.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"hgvs_c": "n.57C>T",
"hgvs_p": null,
"transcript": "ENST00000459935.1",
"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": "ENST00000459935.1"
}
],
"gene_symbol": "PHF7",
"gene_hgnc_id": 18458,
"dbsnp": "rs753391887",
"frequency_reference_population": 0.000019464756,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000187461,
"gnomad_genomes_af": 0.0000262595,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.41786718368530273,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.32,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1503,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.485,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016483.7",
"gene_symbol": "PHF7",
"hgnc_id": 18458,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.583C>T",
"hgvs_p": "p.His195Tyr"
}
],
"clinvar_disease": "Progressive sensorineural hearing impairment",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Progressive sensorineural hearing impairment",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}