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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: 19-1399149-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1399149&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 1399149,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_138924.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "NM_000156.6",
"protein_id": "NP_000147.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 236,
"cds_start": 438,
"cds_end": null,
"cds_length": 711,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1110,
"mane_select": "ENST00000252288.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000156.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "ENST00000252288.8",
"protein_id": "ENSP00000252288.1",
"transcript_support_level": 1,
"aa_start": 146,
"aa_end": null,
"aa_length": 236,
"cds_start": 438,
"cds_end": null,
"cds_length": 711,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1110,
"mane_select": "NM_000156.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252288.8"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.708A>G",
"hgvs_p": "p.Thr236Thr",
"transcript": "ENST00000902474.1",
"protein_id": "ENSP00000572533.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 326,
"cds_start": 708,
"cds_end": null,
"cds_length": 981,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 1304,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902474.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "NM_138924.3",
"protein_id": "NP_620279.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 269,
"cds_start": 438,
"cds_end": null,
"cds_length": 810,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1737,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138924.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "ENST00000447102.8",
"protein_id": "ENSP00000403536.2",
"transcript_support_level": 2,
"aa_start": 146,
"aa_end": null,
"aa_length": 269,
"cds_start": 438,
"cds_end": null,
"cds_length": 810,
"cdna_start": 532,
"cdna_end": null,
"cdna_length": 1769,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447102.8"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "ENST00000902472.1",
"protein_id": "ENSP00000572531.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 237,
"cds_start": 438,
"cds_end": null,
"cds_length": 714,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1049,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902472.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "ENST00000902476.1",
"protein_id": "ENSP00000572535.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 235,
"cds_start": 438,
"cds_end": null,
"cds_length": 708,
"cdna_start": 472,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902476.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.426A>G",
"hgvs_p": "p.Thr142Thr",
"transcript": "ENST00000902475.1",
"protein_id": "ENSP00000572534.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 232,
"cds_start": 426,
"cds_end": null,
"cds_length": 699,
"cdna_start": 465,
"cdna_end": null,
"cdna_length": 1003,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902475.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr",
"transcript": "ENST00000902477.1",
"protein_id": "ENSP00000572536.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 228,
"cds_start": 438,
"cds_end": null,
"cds_length": 687,
"cdna_start": 470,
"cdna_end": null,
"cdna_length": 984,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902477.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.396A>G",
"hgvs_p": "p.Thr132Thr",
"transcript": "ENST00000902471.1",
"protein_id": "ENSP00000572530.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 222,
"cds_start": 396,
"cds_end": null,
"cds_length": 669,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 1006,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902471.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.369A>G",
"hgvs_p": "p.Thr123Thr",
"transcript": "ENST00000640762.1",
"protein_id": "ENSP00000492031.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 213,
"cds_start": 369,
"cds_end": null,
"cds_length": 642,
"cdna_start": 387,
"cdna_end": null,
"cdna_length": 751,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640762.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.369A>G",
"hgvs_p": "p.Thr123Thr",
"transcript": "ENST00000970136.1",
"protein_id": "ENSP00000640195.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 212,
"cds_start": 369,
"cds_end": null,
"cds_length": 639,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 943,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970136.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.318A>G",
"hgvs_p": "p.Thr106Thr",
"transcript": "ENST00000902470.1",
"protein_id": "ENSP00000572529.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 196,
"cds_start": 318,
"cds_end": null,
"cds_length": 591,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 948,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902470.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.228A>G",
"hgvs_p": "p.Thr76Thr",
"transcript": "ENST00000902473.1",
"protein_id": "ENSP00000572532.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 166,
"cds_start": 228,
"cds_end": null,
"cds_length": 501,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 834,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902473.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "c.120A>G",
"hgvs_p": "p.Thr40Thr",
"transcript": "ENST00000591788.3",
"protein_id": "ENSP00000466341.3",
"transcript_support_level": 5,
"aa_start": 40,
"aa_end": null,
"aa_length": 107,
"cds_start": 120,
"cds_end": null,
"cds_length": 324,
"cdna_start": 121,
"cdna_end": null,
"cdna_length": 401,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000591788.3"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"hgvs_c": "n.271A>G",
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000640164.1"
}
],
"gene_symbol": "GAMT",
"gene_hgnc_id": 4136,
"dbsnp": "rs80338733",
"frequency_reference_population": 0.000022929667,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000246326,
"gnomad_genomes_af": 0.00000657246,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.24,
"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": -2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "BP7,PM2_Supporting,BP2,BP4",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 3,
"pathogenic_score": 1,
"criteria": [
"BP7",
"PM2_Supporting",
"BP2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_138924.3",
"gene_symbol": "GAMT",
"hgnc_id": 4136,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.438A>G",
"hgvs_p": "p.Thr146Thr"
}
],
"clinvar_disease": "Cerebral creatine deficiency syndrome,Deficiency of guanidinoacetate methyltransferase",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:2 LB:1 O:1",
"phenotype_combined": "Deficiency of guanidinoacetate methyltransferase|Cerebral creatine deficiency syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}