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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: 3-49419054-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49419054&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AMT",
"hgnc_id": 473,
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_000481.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000283189",
"hgnc_id": null,
"hgvs_c": "c.1031G>A",
"hgvs_p": "p.Arg344His",
"inheritance_mode": "",
"pathogenic_score": 16,
"score": 16,
"transcript": "ENST00000636166.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 16,
"allele_count_reference_population": 23,
"alphamissense_prediction": null,
"alphamissense_score": 0.9327,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.47,
"chr": "3",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Glycine encephalopathy,Glycine encephalopathy 1,Glycine encephalopathy 2,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9412282705307007,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 403,
"aa_ref": "R",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1997,
"cdna_start": 817,
"cds_end": null,
"cds_length": 1212,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_000481.4",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000273588.9",
"protein_coding": true,
"protein_id": "NP_000472.2",
"strand": false,
"transcript": "NM_000481.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 403,
"aa_ref": "R",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1997,
"cdna_start": 817,
"cds_end": null,
"cds_length": 1212,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000273588.9",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000481.4",
"protein_coding": true,
"protein_id": "ENSP00000273588.3",
"strand": false,
"transcript": "ENST00000273588.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 482,
"aa_ref": "R",
"aa_start": 344,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2266,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1449,
"cds_start": 1031,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000636166.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000283189",
"hgvs_c": "c.1031G>A",
"hgvs_p": "p.Arg344His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490106.1",
"strand": false,
"transcript": "ENST00000636166.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 386,
"aa_ref": "R",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1831,
"cdna_start": 898,
"cds_end": null,
"cds_length": 1161,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000395338.7",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378747.2",
"strand": false,
"transcript": "ENST00000395338.7",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 386,
"aa_ref": "R",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1750,
"cdna_start": 817,
"cds_end": null,
"cds_length": 1161,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001164712.2",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158184.1",
"strand": false,
"transcript": "NM_001164712.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 376,
"aa_ref": "R",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1783,
"cdna_start": 723,
"cds_end": null,
"cds_length": 1131,
"cds_start": 713,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000638063.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.713G>A",
"hgvs_p": "p.Arg238His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489760.1",
"strand": false,
"transcript": "ENST00000638063.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 359,
"aa_ref": "R",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1865,
"cdna_start": 685,
"cds_end": null,
"cds_length": 1080,
"cds_start": 662,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001164710.2",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Arg221His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158182.1",
"strand": false,
"transcript": "NM_001164710.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 359,
"aa_ref": "R",
"aa_start": 221,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1860,
"cdna_start": 681,
"cds_end": null,
"cds_length": 1080,
"cds_start": 662,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000458307.6",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.662G>A",
"hgvs_p": "p.Arg221His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415619.2",
"strand": false,
"transcript": "ENST00000458307.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 359,
"aa_ref": "R",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1610,
"cdna_start": 736,
"cds_end": null,
"cds_length": 1080,
"cds_start": 713,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000635808.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.713G>A",
"hgvs_p": "p.Arg238His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489620.1",
"strand": false,
"transcript": "ENST00000635808.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 355,
"aa_ref": "R",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2038,
"cdna_start": 859,
"cds_end": null,
"cds_length": 1068,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000538581.6",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"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": "ENSP00000443200.2",
"strand": false,
"transcript": "ENST00000538581.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 351,
"aa_ref": "R",
"aa_start": 213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1914,
"cdna_start": 785,
"cds_end": null,
"cds_length": 1056,
"cds_start": 638,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000636865.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"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": "ENSP00000490601.1",
"strand": false,
"transcript": "ENST00000636865.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 351,
"aa_ref": "R",
"aa_start": 265,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 801,
"cds_end": null,
"cds_length": 1056,
"cds_start": 794,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000637682.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489856.1",
"strand": false,
"transcript": "ENST00000637682.1",
"transcript_support_level": 5
},
{
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"aa_length": 347,
"aa_ref": "R",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1829,
"cdna_start": 649,
"cds_end": null,
"cds_length": 1044,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001164711.2",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.626G>A",
"hgvs_p": "p.Arg209His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158183.1",
"strand": false,
"transcript": "NM_001164711.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 347,
"aa_ref": "R",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1620,
"cdna_start": 649,
"cds_end": null,
"cds_length": 1044,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000636522.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.626G>A",
"hgvs_p": "p.Arg209His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489758.1",
"strand": false,
"transcript": "ENST00000636522.1",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 338,
"aa_ref": "R",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1646,
"cdna_start": 788,
"cds_end": null,
"cds_length": 1017,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000427987.6",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"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": "ENSP00000403821.2",
"strand": false,
"transcript": "ENST00000427987.6",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 321,
"aa_ref": "R",
"aa_start": 202,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1512,
"cdna_start": 605,
"cds_end": null,
"cds_length": 966,
"cds_start": 605,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000637455.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489628.1",
"strand": false,
"transcript": "ENST00000637455.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
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"aa_length": 257,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1546,
"cdna_start": 366,
"cds_end": null,
"cds_length": 774,
"cds_start": 356,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000636199.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.356G>A",
"hgvs_p": "p.Arg119His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490871.1",
"strand": false,
"transcript": "ENST00000636199.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 242,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1509,
"cdna_start": null,
"cds_end": null,
"cds_length": 729,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000636597.1",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "c.550+656G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490251.1",
"strand": false,
"transcript": "ENST00000636597.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 977,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000399379.7",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "n.*166G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000399943.2",
"strand": false,
"transcript": "ENST00000399379.7",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 798,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000430521.2",
"gene_hgnc_id": 473,
"gene_symbol": "AMT",
"hgvs_c": "n.*596G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000388068.2",
"strand": false,
"transcript": "ENST00000430521.2",
"transcript_support_level": 5
},
{
"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": 3976,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
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