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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: 19-41357947-GCCATGTCC-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41357947&ref=GCCATGTCC&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41357947,
"ref": "GCCATGTCC",
"alt": "G",
"effect": "frameshift_variant",
"transcript": "ENST00000243578.8",
"consequences": [
{
"aa_ref": "GDMA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.156_163delGGACATGG",
"hgvs_p": "p.Asp53fs",
"transcript": "NM_030578.4",
"protein_id": "NP_085055.2",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 175,
"cds_start": 156,
"cds_end": null,
"cds_length": 528,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": "ENST00000243578.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GDMA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.156_163delGGACATGG",
"hgvs_p": "p.Asp53fs",
"transcript": "ENST00000243578.8",
"protein_id": "ENSP00000243578.2",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 175,
"cds_start": 156,
"cds_end": null,
"cds_length": 528,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": "NM_030578.4",
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.-30+6748_-30+6755delATGTCCCC",
"hgvs_p": null,
"transcript": "ENST00000539627.5",
"protein_id": "ENSP00000441900.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 132,
"cds_start": -4,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GDMA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.156_163delGGACATGG",
"hgvs_p": "p.Asp53fs",
"transcript": "ENST00000675972.1",
"protein_id": "ENSP00000501911.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 175,
"cds_start": 156,
"cds_end": null,
"cds_length": 528,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GDMA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.156_163delGGACATGG",
"hgvs_p": "p.Asp53fs",
"transcript": "XM_011527349.3",
"protein_id": "XP_011525651.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 175,
"cds_start": 156,
"cds_end": null,
"cds_length": 528,
"cdna_start": 329,
"cdna_end": null,
"cdna_length": 977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "MA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.-4_4delGGACATGG",
"hgvs_p": "p.Met1fs",
"transcript": "XM_011527350.3",
"protein_id": "XP_011525652.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 122,
"cds_start": 1,
"cds_end": null,
"cds_length": 369,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 915,
"mane_select": null,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.*2_*9delGGACATGG",
"hgvs_p": null,
"transcript": "ENST00000594416.1",
"protein_id": "ENSP00000469666.1",
"transcript_support_level": 3,
"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": 848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.-4_4delGGACATGG",
"hgvs_p": null,
"transcript": "XM_011527350.3",
"protein_id": "XP_011525652.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.*2_*9delGGACATGG",
"hgvs_p": null,
"transcript": "ENST00000594416.1",
"protein_id": "ENSP00000469666.1",
"transcript_support_level": 3,
"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": 848,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.142+3635_142+3642delATGTCCCC",
"hgvs_p": null,
"transcript": "ENST00000604123.5",
"protein_id": "ENSP00000474871.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": -4,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "n.350+6748_350+6755delATGTCCCC",
"hgvs_p": null,
"transcript": "ENST00000604424.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"dbsnp": "rs786204189",
"frequency_reference_population": 0.000013010878,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000136812,
"gnomad_genomes_af": 0.0000065716,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.239,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000243578.8",
"gene_symbol": "B9D2",
"hgnc_id": 28636,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.156_163delGGACATGG",
"hgvs_p": "p.Asp53fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000539627.5",
"gene_symbol": "TMEM91",
"hgnc_id": 32393,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-30+6748_-30+6755delATGTCCCC",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000604424.1",
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.350+6748_350+6755delATGTCCCC",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome,Meckel-Gruber syndrome",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Joubert syndrome|Meckel-Gruber syndrome;Joubert syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}