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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: 19-1397408-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1397408&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "GAMT",
"hgnc_id": 4136,
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Arg221His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_000156.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 60,
"alphamissense_prediction": null,
"alphamissense_score": 0.12,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Cerebral creatine deficiency syndrome,Deficiency of guanidinoacetate methyltransferase,Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.46137627959251404,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": 728,
"cds_end": null,
"cds_length": 711,
"cds_start": 662,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_000156.6",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Arg221His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000252288.8",
"protein_coding": true,
"protein_id": "NP_000147.1",
"strand": false,
"transcript": "NM_000156.6",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "R",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": 728,
"cds_end": null,
"cds_length": 711,
"cds_start": 662,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000252288.8",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Arg221His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000156.6",
"protein_coding": true,
"protein_id": "ENSP00000252288.1",
"strand": false,
"transcript": "ENST00000252288.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 326,
"aa_ref": "R",
"aa_start": 311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1304,
"cdna_start": 990,
"cds_end": null,
"cds_length": 981,
"cds_start": 932,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902474.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.932G>A",
"hgvs_p": "p.Arg311His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572533.1",
"strand": false,
"transcript": "ENST00000902474.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 237,
"aa_ref": "R",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1049,
"cdna_start": 731,
"cds_end": null,
"cds_length": 714,
"cds_start": 665,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902472.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.665G>A",
"hgvs_p": "p.Arg222His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572531.1",
"strand": false,
"transcript": "ENST00000902472.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 235,
"aa_ref": "R",
"aa_start": 220,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1007,
"cdna_start": 693,
"cds_end": null,
"cds_length": 708,
"cds_start": 659,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902476.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.659G>A",
"hgvs_p": "p.Arg220His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572535.1",
"strand": false,
"transcript": "ENST00000902476.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 232,
"aa_ref": "R",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1003,
"cdna_start": 689,
"cds_end": null,
"cds_length": 699,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902475.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.650G>A",
"hgvs_p": "p.Arg217His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572534.1",
"strand": false,
"transcript": "ENST00000902475.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 228,
"aa_ref": "R",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 984,
"cdna_start": 670,
"cds_end": null,
"cds_length": 687,
"cds_start": 638,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902477.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.638G>A",
"hgvs_p": "p.Arg213His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572536.1",
"strand": false,
"transcript": "ENST00000902477.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 222,
"aa_ref": "R",
"aa_start": 207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1006,
"cdna_start": 682,
"cds_end": null,
"cds_length": 669,
"cds_start": 620,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902471.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572530.1",
"strand": false,
"transcript": "ENST00000902471.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 213,
"aa_ref": "R",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 751,
"cdna_start": 611,
"cds_end": null,
"cds_length": 642,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000640762.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.593G>A",
"hgvs_p": "p.Arg198His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492031.1",
"strand": false,
"transcript": "ENST00000640762.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 212,
"aa_ref": "R",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 943,
"cdna_start": 629,
"cds_end": null,
"cds_length": 639,
"cds_start": 590,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000970136.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640195.1",
"strand": false,
"transcript": "ENST00000970136.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 196,
"aa_ref": "R",
"aa_start": 181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 948,
"cdna_start": 627,
"cds_end": null,
"cds_length": 591,
"cds_start": 542,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000902470.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.542G>A",
"hgvs_p": "p.Arg181His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572529.1",
"strand": false,
"transcript": "ENST00000902470.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 166,
"aa_ref": "R",
"aa_start": 151,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 834,
"cdna_start": 510,
"cds_end": null,
"cds_length": 501,
"cds_start": 452,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000902473.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "c.452G>A",
"hgvs_p": "p.Arg151His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572532.1",
"strand": false,
"transcript": "ENST00000902473.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 520,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000640164.1",
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"hgvs_c": "n.495G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000640164.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs766553422",
"effect": "missense_variant",
"frequency_reference_population": 0.000037227772,
"gene_hgnc_id": 4136,
"gene_symbol": "GAMT",
"gnomad_exomes_ac": 47,
"gnomad_exomes_af": 0.0000322027,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 13,
"gnomad_genomes_af": 0.0000854162,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Cerebral creatine deficiency syndrome|Deficiency of guanidinoacetate methyltransferase|Inborn genetic diseases|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.327,
"pos": 1397408,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.497,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000156.6"
}
]
}