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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: X-134377619-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=134377619&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 134377619,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "ENST00000370803.8",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001015877.2",
"protein_id": "NP_001015877.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 365,
"cds_start": 2,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4430,
"mane_select": "ENST00000370803.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000370803.8",
"protein_id": "ENSP00000359839.4",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 365,
"cds_start": 2,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4430,
"mane_select": "NM_001015877.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000332070.7",
"protein_id": "ENSP00000329097.3",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 365,
"cds_start": 2,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000370799.5",
"protein_id": "ENSP00000359835.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 324,
"cds_start": 2,
"cds_end": null,
"cds_length": 975,
"cdna_start": 196,
"cdna_end": null,
"cdna_length": 4186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000370800.4",
"protein_id": "ENSP00000359836.4",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 312,
"cds_start": 2,
"cds_end": null,
"cds_length": 939,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 1150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000625464.2",
"protein_id": "ENSP00000487420.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 366,
"cds_start": 2,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_032458.3",
"protein_id": "NP_115834.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 365,
"cds_start": 2,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4760,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000691812.1",
"protein_id": "ENSP00000510211.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 365,
"cds_start": 2,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 189,
"cdna_end": null,
"cdna_length": 3892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000687496.1",
"protein_id": "ENSP00000509551.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 331,
"cds_start": 2,
"cds_end": null,
"cds_length": 996,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 4335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000688598.1",
"protein_id": "ENSP00000510410.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 331,
"cds_start": 2,
"cds_end": null,
"cds_length": 996,
"cdna_start": 182,
"cdna_end": null,
"cdna_length": 4614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_032335.3",
"protein_id": "NP_115711.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 312,
"cds_start": 2,
"cds_end": null,
"cds_length": 939,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 1211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000685047.1",
"protein_id": "ENSP00000509894.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 156,
"cds_start": 2,
"cds_end": null,
"cds_length": 471,
"cdna_start": 228,
"cdna_end": null,
"cdna_length": 3790,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000685553.1",
"protein_id": "ENSP00000510193.1",
"transcript_support_level": null,
"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": 4938,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "n.175T>C",
"hgvs_p": null,
"transcript": "ENST00000687834.1",
"protein_id": null,
"transcript_support_level": null,
"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": 5616,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000693759.1",
"protein_id": "ENSP00000509518.1",
"transcript_support_level": null,
"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": 4758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF6",
"gene_hgnc_id": 18145,
"dbsnp": "rs132630300",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9923698306083679,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.781,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.61,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.421,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000370803.8",
"gene_symbol": "PHF6",
"hgnc_id": 18145,
"effects": [
"start_lost"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": "Borjeson-Forssman-Lehmann syndrome,Hereditary spastic paraplegia 4,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Borjeson-Forssman-Lehmann syndrome|Hereditary spastic paraplegia 4|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}