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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-18647303-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=18647303&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 18647303,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000379984.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.214G>A",
"hgvs_p": "p.Glu72Lys",
"transcript": "NM_000330.4",
"protein_id": "NP_000321.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 224,
"cds_start": 214,
"cds_end": null,
"cds_length": 675,
"cdna_start": 254,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "ENST00000379984.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.214G>A",
"hgvs_p": "p.Glu72Lys",
"transcript": "ENST00000379984.4",
"protein_id": "ENSP00000369320.3",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 224,
"cds_start": 214,
"cds_end": null,
"cds_length": 675,
"cdna_start": 254,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": "NM_000330.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "n.705G>A",
"hgvs_p": null,
"transcript": "ENST00000476595.1",
"protein_id": null,
"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": 1246,
"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": 22,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2797+1213C>T",
"hgvs_p": null,
"transcript": "ENST00000379989.6",
"protein_id": "ENSP00000369325.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3463,
"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": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2797+1213C>T",
"hgvs_p": null,
"transcript": "ENST00000379996.7",
"protein_id": "ENSP00000369332.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"hgvs_c": "c.118G>A",
"hgvs_p": "p.Glu40Lys",
"transcript": "XM_047442337.1",
"protein_id": "XP_047298293.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 192,
"cds_start": 118,
"cds_end": null,
"cds_length": 579,
"cdna_start": 374,
"cdna_end": null,
"cdna_length": 2922,
"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": 22,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2797+1213C>T",
"hgvs_p": null,
"transcript": "NM_001037343.2",
"protein_id": "NP_001032420.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3427,
"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": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "CDKL5",
"gene_hgnc_id": 11411,
"hgvs_c": "c.2797+1213C>T",
"hgvs_p": null,
"transcript": "NM_003159.3",
"protein_id": "NP_003150.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RS1",
"gene_hgnc_id": 10457,
"dbsnp": "rs104894928",
"frequency_reference_population": 0.000004554999,
"hom_count_reference_population": 1,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.000004555,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.983725905418396,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.921,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9184,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.67,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.565,
"phylop100way_prediction": "Pathogenic",
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS4,PP3_Moderate,PP1_Strong,PS3_Supporting,PP4,PM1",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PS4",
"PP3_Moderate",
"PP1_Strong",
"PS3_Supporting",
"PP4",
"PM1"
],
"verdict": "Pathogenic",
"transcript": "ENST00000379984.4",
"gene_symbol": "RS1",
"hgnc_id": 10457,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.214G>A",
"hgvs_p": "p.Glu72Lys"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_003159.3",
"gene_symbol": "CDKL5",
"hgnc_id": 11411,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2797+1213C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Juvenile retinoschisis,Retinal dystrophy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:12 LP:1 O:1",
"phenotype_combined": "Juvenile retinoschisis|not provided|Inborn genetic diseases|Retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}