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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: 19-42297316-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=42297316&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 42297316,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002573.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "NM_002573.4",
"protein_id": "NP_002564.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262890.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002573.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "ENST00000262890.8",
"protein_id": "ENSP00000262890.2",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002573.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262890.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "NM_001145939.2",
"protein_id": "NP_001139411.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145939.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "NM_001145940.1",
"protein_id": "NP_001139412.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145940.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "ENST00000538771.5",
"protein_id": "ENSP00000444935.1",
"transcript_support_level": 2,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538771.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "ENST00000877854.1",
"protein_id": "ENSP00000547913.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 231,
"cds_start": 458,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877854.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.452G>A",
"hgvs_p": "p.Arg151Gln",
"transcript": "ENST00000916656.1",
"protein_id": "ENSP00000586715.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 229,
"cds_start": 452,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916656.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "ENST00000877855.1",
"protein_id": "ENSP00000547914.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 218,
"cds_start": 419,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877855.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.392G>A",
"hgvs_p": "p.Arg131Gln",
"transcript": "ENST00000916659.1",
"protein_id": "ENSP00000586718.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 209,
"cds_start": 392,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916659.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.368G>A",
"hgvs_p": "p.Arg123Gln",
"transcript": "ENST00000594989.5",
"protein_id": "ENSP00000471933.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 201,
"cds_start": 368,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000594989.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Gln",
"transcript": "ENST00000916658.1",
"protein_id": "ENSP00000586717.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 192,
"cds_start": 341,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916658.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.335G>A",
"hgvs_p": "p.Arg112Gln",
"transcript": "ENST00000916662.1",
"protein_id": "ENSP00000586721.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 190,
"cds_start": 335,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916662.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107Gln",
"transcript": "ENST00000916661.1",
"protein_id": "ENSP00000586720.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 185,
"cds_start": 320,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916661.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.302G>A",
"hgvs_p": "p.Arg101Gln",
"transcript": "ENST00000916657.1",
"protein_id": "ENSP00000586716.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 179,
"cds_start": 302,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916657.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.269G>A",
"hgvs_p": "p.Arg90Gln",
"transcript": "ENST00000916660.1",
"protein_id": "ENSP00000586719.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 168,
"cds_start": 269,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916660.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln",
"transcript": "ENST00000595530.5",
"protein_id": "ENSP00000473065.1",
"transcript_support_level": 2,
"aa_start": 153,
"aa_end": null,
"aa_length": 163,
"cds_start": 458,
"cds_end": null,
"cds_length": 494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595530.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.218G>A",
"hgvs_p": "p.Arg73Gln",
"transcript": "ENST00000877856.1",
"protein_id": "ENSP00000547915.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 151,
"cds_start": 218,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877856.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "XM_017026846.2",
"protein_id": "XP_016882335.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 218,
"cds_start": 419,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026846.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "XM_017026847.2",
"protein_id": "XP_016882336.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 218,
"cds_start": 419,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026847.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.Arg140Gln",
"transcript": "XM_017026848.1",
"protein_id": "XP_016882337.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 218,
"cds_start": 419,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026848.1"
},
{
"aa_ref": "?",
"aa_alt": "?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.419G>A",
"hgvs_p": "p.???140???",
"transcript": "ENST00000596265.5",
"protein_id": "ENSP00000470753.1",
"transcript_support_level": 3,
"aa_start": 140,
"aa_end": null,
"aa_length": 138,
"cds_start": 419,
"cds_end": null,
"cds_length": 419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596265.5"
}
],
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"dbsnp": "rs773879190",
"frequency_reference_population": 0.000009298439,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.0000088981,
"gnomad_genomes_af": 0.0000131416,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.033427417278289795,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.009,
"revel_prediction": "Benign",
"alphamissense_score": 0.0785,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.368,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_002573.4",
"gene_symbol": "PAFAH1B3",
"hgnc_id": 8576,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}