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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: 17-58210669-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58210669&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "MKS1",
"hgnc_id": 7121,
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_001321269.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
"acmg_score": -11,
"allele_count_reference_population": 1209,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " type 1,Bardet-Biedl syndrome 13,Joubert syndrome,Meckel syndrome,Meckel-Gruber syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.061000000685453415,
"computational_source_selected": "REVEL",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 559,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2343,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_017777.4",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000393119.7",
"protein_coding": true,
"protein_id": "NP_060247.2",
"strand": false,
"transcript": "NM_017777.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 559,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2343,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000393119.7",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017777.4",
"protein_coding": true,
"protein_id": "ENSP00000376827.2",
"strand": false,
"transcript": "ENST00000393119.7",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 416,
"aa_ref": "L",
"aa_start": 195,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2083,
"cdna_start": 1078,
"cds_end": null,
"cds_length": 1251,
"cds_start": 585,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000537529.7",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.585G>A",
"hgvs_p": "p.Leu195Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000442096.3",
"strand": false,
"transcript": "ENST00000537529.7",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 570,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2350,
"cdna_start": 1020,
"cds_end": null,
"cds_length": 1713,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000966002.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636061.1",
"strand": false,
"transcript": "ENST00000966002.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 561,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2260,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1686,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001321269.2",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308198.1",
"strand": false,
"transcript": "NM_001321269.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 561,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2260,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1686,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000678463.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502984.1",
"strand": false,
"transcript": "ENST00000678463.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 551,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2407,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1656,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000872459.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542518.1",
"strand": false,
"transcript": "ENST00000872459.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 540,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 1037,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000872460.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542519.1",
"strand": false,
"transcript": "ENST00000872460.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 516,
"aa_ref": "L",
"aa_start": 295,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2214,
"cdna_start": 910,
"cds_end": null,
"cds_length": 1551,
"cds_start": 885,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000676787.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.885G>A",
"hgvs_p": "p.Leu295Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000503999.1",
"strand": false,
"transcript": "ENST00000676787.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 470,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1626,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000585134.2",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000463826.2",
"strand": false,
"transcript": "ENST00000585134.2",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 456,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2126,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001330397.2",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317326.1",
"strand": false,
"transcript": "NM_001330397.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 456,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2126,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1371,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000313863.11",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000316631.6",
"strand": false,
"transcript": "ENST00000313863.11",
"transcript_support_level": 5
},
{
"aa_alt": "L",
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"aa_length": 432,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1467,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1299,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001411113.1",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001398042.1",
"strand": false,
"transcript": "NM_001411113.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 432,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1467,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1299,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000580127.6",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462423.2",
"strand": false,
"transcript": "ENST00000580127.6",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 356,
"aa_ref": "L",
"aa_start": 135,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2245,
"cdna_start": 941,
"cds_end": null,
"cds_length": 1071,
"cds_start": 405,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001321268.2",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.405G>A",
"hgvs_p": "p.Leu135Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308197.1",
"strand": false,
"transcript": "NM_001321268.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 343,
"aa_ref": "L",
"aa_start": 338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1289,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1032,
"cds_start": 1014,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000581761.6",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1014G>A",
"hgvs_p": "p.Leu338Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462129.2",
"strand": false,
"transcript": "ENST00000581761.6",
"transcript_support_level": 3
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 227,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1158,
"cdna_start": 491,
"cds_end": null,
"cds_length": 684,
"cds_start": 489,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000577824.5",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.489G>A",
"hgvs_p": "p.Leu163Leu",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000462460.1",
"strand": false,
"transcript": "ENST00000577824.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
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"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2269,
"cdna_start": 1048,
"cds_end": null,
"cds_length": 1695,
"cds_start": 1023,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011524957.3",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1023G>A",
"hgvs_p": "p.Leu341Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523259.1",
"strand": false,
"transcript": "XM_011524957.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
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"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2352,
"cdna_start": 1048,
"cds_end": null,
"cds_length": 1689,
"cds_start": 1023,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011524958.3",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1023G>A",
"hgvs_p": "p.Leu341Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523260.1",
"strand": false,
"transcript": "XM_011524958.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 435,
"aa_ref": "L",
"aa_start": 341,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1476,
"cdna_start": 1048,
"cds_end": null,
"cds_length": 1308,
"cds_start": 1023,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011524960.3",
"gene_hgnc_id": 7121,
"gene_symbol": "MKS1",
"hgvs_c": "c.1023G>A",
"hgvs_p": "p.Leu341Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011523262.1",
"strand": false,
"transcript": "XM_011524960.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 418,
"aa_ref": "L",
"aa_start": 195,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1961,
"cdna_start": 740,
"cds_end": null,
"cds_length": 1257,
"cds_start": 585,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
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},
{
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],
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"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Meckel syndrome, type 1|Bardet-Biedl syndrome 13|Meckel-Gruber syndrome;Joubert syndrome|not provided",
"phylop100way_prediction": "Benign",
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}
]
}