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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: 19-1397495-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1397495&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 1397495,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000156.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Thr192Met",
"transcript": "NM_000156.6",
"protein_id": "NP_000147.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 236,
"cds_start": 575,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000252288.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000156.6"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Thr192Met",
"transcript": "ENST00000252288.8",
"protein_id": "ENSP00000252288.1",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 236,
"cds_start": 575,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000156.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252288.8"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.845C>T",
"hgvs_p": "p.Thr282Met",
"transcript": "ENST00000902474.1",
"protein_id": "ENSP00000572533.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 326,
"cds_start": 845,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902474.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.578C>T",
"hgvs_p": "p.Thr193Met",
"transcript": "ENST00000902472.1",
"protein_id": "ENSP00000572531.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 237,
"cds_start": 578,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902472.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.563C>T",
"hgvs_p": "p.Thr188Met",
"transcript": "ENST00000902475.1",
"protein_id": "ENSP00000572534.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 232,
"cds_start": 563,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902475.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Thr184Met",
"transcript": "ENST00000902477.1",
"protein_id": "ENSP00000572536.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 228,
"cds_start": 551,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902477.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Thr178Met",
"transcript": "ENST00000902471.1",
"protein_id": "ENSP00000572530.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 222,
"cds_start": 533,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902471.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.506C>T",
"hgvs_p": "p.Thr169Met",
"transcript": "ENST00000640762.1",
"protein_id": "ENSP00000492031.1",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 213,
"cds_start": 506,
"cds_end": null,
"cds_length": 642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640762.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.455C>T",
"hgvs_p": "p.Thr152Met",
"transcript": "ENST00000902470.1",
"protein_id": "ENSP00000572529.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 196,
"cds_start": 455,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902470.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.365C>T",
"hgvs_p": "p.Thr122Met",
"transcript": "ENST00000902473.1",
"protein_id": "ENSP00000572532.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 166,
"cds_start": 365,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902473.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.572C>T",
"hgvs_p": "p.Thr191Met",
"transcript": "ENST00000902476.1",
"protein_id": "ENSP00000572535.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 235,
"cds_start": 572,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902476.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.503C>T",
"hgvs_p": "p.Thr168Met",
"transcript": "ENST00000970136.1",
"protein_id": "ENSP00000640195.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 212,
"cds_start": 503,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970136.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "n.408C>T",
"hgvs_p": null,
"transcript": "ENST00000640164.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000640164.1"
}
],
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"dbsnp": "rs141066224",
"frequency_reference_population": 0.00008294501,
"hom_count_reference_population": 0,
"allele_count_reference_population": 133,
"gnomad_exomes_af": 0.0000771822,
"gnomad_genomes_af": 0.000137831,
"gnomad_exomes_ac": 112,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3419598340988159,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.677,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3628,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.539,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.11,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,PM2_Supporting",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3",
"PM2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000156.6",
"gene_symbol": "GAMT",
"hgnc_id": 4136,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Thr192Met"
}
],
"clinvar_disease": "Cerebral creatine deficiency syndrome,Deficiency of guanidinoacetate methyltransferase,Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:7 LB:1",
"phenotype_combined": "not provided|Cerebral creatine deficiency syndrome|Deficiency of guanidinoacetate methyltransferase|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}