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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: 17-58206158-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58206158&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 58206158,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017777.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1601G>A",
"hgvs_p": "p.Arg534Gln",
"transcript": "NM_017777.4",
"protein_id": "NP_060247.2",
"transcript_support_level": null,
"aa_start": 534,
"aa_end": null,
"aa_length": 559,
"cds_start": 1601,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393119.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017777.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1601G>A",
"hgvs_p": "p.Arg534Gln",
"transcript": "ENST00000393119.7",
"protein_id": "ENSP00000376827.2",
"transcript_support_level": 1,
"aa_start": 534,
"aa_end": null,
"aa_length": 559,
"cds_start": 1601,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017777.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393119.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1172G>A",
"hgvs_p": "p.Arg391Gln",
"transcript": "ENST00000537529.7",
"protein_id": "ENSP00000442096.3",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 416,
"cds_start": 1172,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537529.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1634G>A",
"hgvs_p": "p.Arg545Gln",
"transcript": "ENST00000966002.1",
"protein_id": "ENSP00000636061.1",
"transcript_support_level": null,
"aa_start": 545,
"aa_end": null,
"aa_length": 570,
"cds_start": 1634,
"cds_end": null,
"cds_length": 1713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966002.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1577G>A",
"hgvs_p": "p.Arg526Gln",
"transcript": "ENST00000872459.1",
"protein_id": "ENSP00000542518.1",
"transcript_support_level": null,
"aa_start": 526,
"aa_end": null,
"aa_length": 551,
"cds_start": 1577,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872459.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1544G>A",
"hgvs_p": "p.Arg515Gln",
"transcript": "ENST00000872460.1",
"protein_id": "ENSP00000542519.1",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 540,
"cds_start": 1544,
"cds_end": null,
"cds_length": 1623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872460.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1472G>A",
"hgvs_p": "p.Arg491Gln",
"transcript": "ENST00000676787.1",
"protein_id": "ENSP00000503999.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 516,
"cds_start": 1472,
"cds_end": null,
"cds_length": 1551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676787.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.992G>A",
"hgvs_p": "p.Arg331Gln",
"transcript": "NM_001321268.2",
"protein_id": "NP_001308197.1",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 356,
"cds_start": 992,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321268.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1610G>A",
"hgvs_p": "p.Arg537Gln",
"transcript": "XM_011524958.3",
"protein_id": "XP_011523260.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 562,
"cds_start": 1610,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524958.3"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1518G>A",
"hgvs_p": "p.Ser506Ser",
"transcript": "NM_001321269.2",
"protein_id": "NP_001308198.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 561,
"cds_start": 1518,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321269.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1518G>A",
"hgvs_p": "p.Ser506Ser",
"transcript": "ENST00000678463.1",
"protein_id": "ENSP00000502984.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 561,
"cds_start": 1518,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678463.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1527G>A",
"hgvs_p": "p.Ser509Ser",
"transcript": "XM_011524957.3",
"protein_id": "XP_011523259.1",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 564,
"cds_start": 1527,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011524957.3"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1089G>A",
"hgvs_p": "p.Ser363Ser",
"transcript": "XM_005257485.5",
"protein_id": "XP_005257542.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 418,
"cds_start": 1089,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005257485.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.909G>A",
"hgvs_p": "p.Ser303Ser",
"transcript": "XM_047436333.1",
"protein_id": "XP_047292289.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 358,
"cds_start": 909,
"cds_end": null,
"cds_length": 1077,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436333.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.*13G>A",
"hgvs_p": null,
"transcript": "NM_001330397.2",
"protein_id": "NP_001317326.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 456,
"cds_start": null,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330397.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.*13G>A",
"hgvs_p": null,
"transcript": "ENST00000313863.11",
"protein_id": "ENSP00000316631.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 456,
"cds_start": null,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000313863.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*1008G>A",
"hgvs_p": null,
"transcript": "ENST00000393120.6",
"protein_id": "ENSP00000376828.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000393120.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.427G>A",
"hgvs_p": null,
"transcript": "ENST00000583577.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000583577.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*1220G>A",
"hgvs_p": null,
"transcript": "ENST00000675753.2",
"protein_id": "ENSP00000502156.1",
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675753.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*1075G>A",
"hgvs_p": null,
"transcript": "ENST00000677111.1",
"protein_id": "ENSP00000504282.1",
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000677111.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.2875G>A",
"hgvs_p": null,
"transcript": "ENST00000677160.1",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000677160.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.2922G>A",
"hgvs_p": null,
"transcript": "ENST00000677416.1",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000677416.1"
},
{
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"computational_score_selected": 0.01651272177696228,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1064,
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"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.096,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
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"pathogenic_score": 0,
"criteria": [
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"BP6"
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"verdict": "Likely_benign",
"transcript": "NM_017777.4",
"gene_symbol": "MKS1",
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"effects": [
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],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1601G>A",
"hgvs_p": "p.Arg534Gln"
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],
"clinvar_disease": " type 1,Bardet-Biedl syndrome 13,Joubert syndrome,Joubert syndrome 28,MKS1-related disorder,Meckel syndrome,Meckel-Gruber syndrome,Microcephaly,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Bardet-Biedl syndrome 13|not provided|not specified|Meckel-Gruber syndrome;Joubert syndrome|Microcephaly|MKS1-related disorder|Meckel syndrome, type 1|Joubert syndrome 28;Bardet-Biedl syndrome 13;Meckel syndrome, type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}