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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: 19-41363487-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41363487&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41363487,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000243578.8",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.33A>G",
"hgvs_p": "p.Ile11Met",
"transcript": "NM_030578.4",
"protein_id": "NP_085055.2",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 175,
"cds_start": 33,
"cds_end": null,
"cds_length": 528,
"cdna_start": 229,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": "ENST00000243578.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.33A>G",
"hgvs_p": "p.Ile11Met",
"transcript": "ENST00000243578.8",
"protein_id": "ENSP00000243578.2",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 175,
"cds_start": 33,
"cds_end": null,
"cds_length": 528,
"cdna_start": 229,
"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+12285T>C",
"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": "I",
"aa_alt": "M",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.33A>G",
"hgvs_p": "p.Ile11Met",
"transcript": "ENST00000675972.1",
"protein_id": "ENSP00000501911.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 175,
"cds_start": 33,
"cds_end": null,
"cds_length": 528,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.33A>G",
"hgvs_p": "p.Ile11Met",
"transcript": "XM_011527349.3",
"protein_id": "XP_011525651.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 175,
"cds_start": 33,
"cds_end": null,
"cds_length": 528,
"cdna_start": 199,
"cdna_end": null,
"cdna_length": 977,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.33A>G",
"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": false,
"strand": false,
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.172A>G",
"hgvs_p": null,
"transcript": "ENST00000601597.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 421,
"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+9172T>C",
"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+12285T>C",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.-72+471A>G",
"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
}
],
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"dbsnp": "rs2241714",
"frequency_reference_population": 0.6833035,
"hom_count_reference_population": 380889,
"allele_count_reference_population": 1102558,
"gnomad_exomes_af": 0.681294,
"gnomad_genomes_af": 0.702648,
"gnomad_exomes_ac": 995851,
"gnomad_genomes_ac": 106707,
"gnomad_exomes_homalt": 342556,
"gnomad_genomes_homalt": 38333,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 7.400341246466269e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.081,
"revel_prediction": "Benign",
"alphamissense_score": 0.0736,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.146,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000243578.8",
"gene_symbol": "B9D2",
"hgnc_id": 28636,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.33A>G",
"hgvs_p": "p.Ile11Met"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000539627.5",
"gene_symbol": "TMEM91",
"hgnc_id": 32393,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-30+12285T>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000604424.1",
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.350+12285T>C",
"hgvs_p": null
}
],
"clinvar_disease": " type 10,Joubert syndrome,Meckel syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Meckel syndrome, type 10|Joubert syndrome;Meckel-Gruber syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}