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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: 17-50194032-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50194032&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL1A1",
"hgnc_id": 2197,
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"inheritance_mode": "AD",
"pathogenic_score": 23,
"score": 23,
"transcript": "NM_000088.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_score": 23,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.5928,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.59,
"chr": "17",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "COL1A1-related disorder,Ehlers-Danlos syndrome,Osteogenesis imperfecta,Osteogenesis imperfecta type I,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9934141635894775,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1464,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5914,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4395,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "NM_000088.4",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000225964.10",
"protein_coding": true,
"protein_id": "NP_000079.2",
"strand": false,
"transcript": "NM_000088.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1464,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5914,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4395,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000225964.10",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000088.4",
"protein_coding": true,
"protein_id": "ENSP00000225964.6",
"strand": false,
"transcript": "ENST00000225964.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4778,
"cdna_start": 1794,
"cds_end": null,
"cds_length": 4392,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861334.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531393.1",
"strand": false,
"transcript": "ENST00000861334.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4765,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4392,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861339.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531398.1",
"strand": false,
"transcript": "ENST00000861339.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1459,
"aa_ref": "G",
"aa_start": 555,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4752,
"cdna_start": 1784,
"cds_end": null,
"cds_length": 4380,
"cds_start": 1663,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861340.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1663G>A",
"hgvs_p": "p.Gly555Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531399.1",
"strand": false,
"transcript": "ENST00000861340.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1452,
"aa_ref": "G",
"aa_start": 548,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4732,
"cdna_start": 1760,
"cds_end": null,
"cds_length": 4359,
"cds_start": 1642,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000861338.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1642G>A",
"hgvs_p": "p.Gly548Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531397.1",
"strand": false,
"transcript": "ENST00000861338.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1446,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4714,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4341,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861336.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531395.1",
"strand": false,
"transcript": "ENST00000861336.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1446,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4710,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4341,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861342.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531401.1",
"strand": false,
"transcript": "ENST00000861342.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1431,
"aa_ref": "G",
"aa_start": 527,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4687,
"cdna_start": 1696,
"cds_end": null,
"cds_length": 4296,
"cds_start": 1579,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000919350.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1579G>A",
"hgvs_p": "p.Gly527Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589409.1",
"strand": false,
"transcript": "ENST00000919350.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1428,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4656,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4287,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861343.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531402.1",
"strand": false,
"transcript": "ENST00000861343.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1422,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4642,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4269,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861337.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531396.1",
"strand": false,
"transcript": "ENST00000861337.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 1419,
"aa_ref": "G",
"aa_start": 515,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4627,
"cdna_start": 1659,
"cds_end": null,
"cds_length": 4260,
"cds_start": 1543,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000861344.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1543G>A",
"hgvs_p": "p.Gly515Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531403.1",
"strand": false,
"transcript": "ENST00000861344.1",
"transcript_support_level": null
},
{
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"aa_length": 930,
"aa_ref": "G",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3182,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 2793,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861333.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531392.1",
"strand": false,
"transcript": "ENST00000861333.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1398,
"aa_ref": "G",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5716,
"cdna_start": 1598,
"cds_end": null,
"cds_length": 4197,
"cds_start": 1480,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011524341.2",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Gly494Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011522643.1",
"strand": false,
"transcript": "XM_011524341.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1374,
"aa_ref": "G",
"aa_start": 560,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5644,
"cdna_start": 1796,
"cds_end": null,
"cds_length": 4125,
"cds_start": 1678,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_005257058.5",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1678G>A",
"hgvs_p": "p.Gly560Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257115.2",
"strand": false,
"transcript": "XM_005257058.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1203,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3981,
"cdna_start": null,
"cds_end": null,
"cds_length": 3612,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 40,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861341.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1668+98G>A",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531400.1",
"strand": false,
"transcript": "ENST00000861341.1",
"transcript_support_level": null
},
{
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"aa_end": null,
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3589,
"cdna_start": null,
"cds_end": null,
"cds_length": 3216,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 35,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000861335.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1056+1891G>A",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531394.1",
"strand": false,
"transcript": "ENST00000861335.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3106,
"cdna_start": null,
"cds_end": null,
"cds_length": 2766,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000963828.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.1093+1597G>A",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633887.1",
"strand": false,
"transcript": "ENST00000963828.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4996,
"cdna_start": null,
"cds_end": null,
"cds_length": 3477,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005257059.5",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.958-1339G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257116.2",
"strand": false,
"transcript": "XM_005257059.5",
"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": 614,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000463440.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "n.68G>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": "ENST00000463440.1",
"transcript_support_level": 2
},
{
"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": 1192,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
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{
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],
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"phenotype_combined": "not provided|Osteogenesis imperfecta type I|Osteogenesis imperfecta|Ehlers-Danlos syndrome|COL1A1-related disorder",
"phylop100way_prediction": "Pathogenic",
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}
]
}