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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: 2-227007369-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227007369&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227007369,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000092.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.5029C>T",
"hgvs_p": "p.Arg1677Cys",
"transcript": "NM_000092.5",
"protein_id": "NP_000083.3",
"transcript_support_level": null,
"aa_start": 1677,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5029,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396625.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000092.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.5029C>T",
"hgvs_p": "p.Arg1677Cys",
"transcript": "ENST00000396625.5",
"protein_id": "ENSP00000379866.3",
"transcript_support_level": 5,
"aa_start": 1677,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5029,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000092.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396625.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.631C>T",
"hgvs_p": "p.Arg211Cys",
"transcript": "ENST00000682098.1",
"protein_id": "ENSP00000508331.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 224,
"cds_start": 631,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682098.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.5029C>T",
"hgvs_p": "p.Arg1677Cys",
"transcript": "XM_005246281.4",
"protein_id": "XP_005246338.1",
"transcript_support_level": null,
"aa_start": 1677,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5029,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005246281.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.5029C>T",
"hgvs_p": "p.Arg1677Cys",
"transcript": "XM_047443228.1",
"protein_id": "XP_047299184.1",
"transcript_support_level": null,
"aa_start": 1677,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5029,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443228.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4948C>T",
"hgvs_p": "p.Arg1650Cys",
"transcript": "XM_011510557.3",
"protein_id": "XP_011508859.1",
"transcript_support_level": null,
"aa_start": 1650,
"aa_end": null,
"aa_length": 1663,
"cds_start": 4948,
"cds_end": null,
"cds_length": 4992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510557.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4921C>T",
"hgvs_p": "p.Arg1641Cys",
"transcript": "XM_011510558.3",
"protein_id": "XP_011508860.1",
"transcript_support_level": null,
"aa_start": 1641,
"aa_end": null,
"aa_length": 1654,
"cds_start": 4921,
"cds_end": null,
"cds_length": 4965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510558.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4912C>T",
"hgvs_p": "p.Arg1638Cys",
"transcript": "XM_017003297.2",
"protein_id": "XP_016858786.1",
"transcript_support_level": null,
"aa_start": 1638,
"aa_end": null,
"aa_length": 1651,
"cds_start": 4912,
"cds_end": null,
"cds_length": 4956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003297.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4840C>T",
"hgvs_p": "p.Arg1614Cys",
"transcript": "XM_006712246.4",
"protein_id": "XP_006712309.1",
"transcript_support_level": null,
"aa_start": 1614,
"aa_end": null,
"aa_length": 1627,
"cds_start": 4840,
"cds_end": null,
"cds_length": 4884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712246.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4474C>T",
"hgvs_p": "p.Arg1492Cys",
"transcript": "XM_005246282.4",
"protein_id": "XP_005246339.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 1505,
"cds_start": 4474,
"cds_end": null,
"cds_length": 4518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005246282.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.3355C>T",
"hgvs_p": "p.Arg1119Cys",
"transcript": "XM_011510572.4",
"protein_id": "XP_011508874.1",
"transcript_support_level": null,
"aa_start": 1119,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3355,
"cds_end": null,
"cds_length": 3399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510572.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_011510559.3",
"protein_id": "XP_011508861.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1612,
"cds_start": null,
"cds_end": null,
"cds_length": 4839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510559.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_011510560.3",
"protein_id": "XP_011508862.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1612,
"cds_start": null,
"cds_end": null,
"cds_length": 4839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510560.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_047443241.1",
"protein_id": "XP_047299197.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1612,
"cds_start": null,
"cds_end": null,
"cds_length": 4839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443241.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_047443242.1",
"protein_id": "XP_047299198.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1612,
"cds_start": null,
"cds_end": null,
"cds_length": 4839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443242.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_011510561.3",
"protein_id": "XP_011508863.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1608,
"cds_start": null,
"cds_end": null,
"cds_length": 4827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510561.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_011510562.3",
"protein_id": "XP_011508864.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1608,
"cds_start": null,
"cds_end": null,
"cds_length": 4827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510562.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": 47,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4809+649C>T",
"hgvs_p": null,
"transcript": "XM_047443245.1",
"protein_id": "XP_047299201.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1608,
"cds_start": null,
"cds_end": null,
"cds_length": 4827,
"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443245.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4216+14679C>T",
"hgvs_p": null,
"transcript": "XM_011510565.3",
"protein_id": "XP_011508867.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1424,
"cds_start": null,
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"cds_length": 4275,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510565.3"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4216+14679C>T",
"hgvs_p": null,
"transcript": "XM_011510566.3",
"protein_id": "XP_011508868.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": null,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510566.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4216+14679C>T",
"hgvs_p": null,
"transcript": "XM_011510567.3",
"protein_id": "XP_011508869.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1420,
"cds_start": null,
"cds_end": null,
"cds_length": 4263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510567.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": 44,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4216+14679C>T",
"hgvs_p": null,
"transcript": "XM_047443248.1",
"protein_id": "XP_047299204.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1420,
"cds_start": null,
"cds_end": null,
"cds_length": 4263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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],
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"computational_score_selected": 0.6181402206420898,
"computational_prediction_selected": "Uncertain_significance",
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"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.76,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.349,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.751,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_classification": "Likely_benign",
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{
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"criteria": [
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"verdict": "Likely_benign",
"transcript": "NM_000092.5",
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"effects": [
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],
"clinvar_disease": " 1, benign familial,Autosomal recessive Alport syndrome,Hematuria,X-linked Alport syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Autosomal recessive Alport syndrome|not provided|X-linked Alport syndrome|Autosomal recessive Alport syndrome;Hematuria, benign familial, 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}