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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: 2-240877543-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=240877543&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 240877543,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_000030.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "NM_000030.3",
"protein_id": "NP_000021.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 392,
"cds_start": 853,
"cds_end": null,
"cds_length": 1179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307503.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000030.3"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "ENST00000307503.4",
"protein_id": "ENSP00000302620.3",
"transcript_support_level": 1,
"aa_start": 285,
"aa_end": null,
"aa_length": 392,
"cds_start": 853,
"cds_end": null,
"cds_length": 1179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000030.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307503.4"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.1126G>T",
"hgvs_p": "p.Glu376*",
"transcript": "ENST00000908235.1",
"protein_id": "ENSP00000578294.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 483,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908235.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.1042G>T",
"hgvs_p": "p.Glu348*",
"transcript": "ENST00000908236.1",
"protein_id": "ENSP00000578295.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 455,
"cds_start": 1042,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908236.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.1000G>T",
"hgvs_p": "p.Glu334*",
"transcript": "ENST00000908246.1",
"protein_id": "ENSP00000578305.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 441,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908246.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.934G>T",
"hgvs_p": "p.Glu312*",
"transcript": "ENST00000908247.1",
"protein_id": "ENSP00000578306.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 419,
"cds_start": 934,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908247.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "ENST00000908244.1",
"protein_id": "ENSP00000578303.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 417,
"cds_start": 853,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908244.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.904G>T",
"hgvs_p": "p.Glu302*",
"transcript": "ENST00000908232.1",
"protein_id": "ENSP00000578291.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 409,
"cds_start": 904,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908232.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.895G>T",
"hgvs_p": "p.Glu299*",
"transcript": "ENST00000908229.1",
"protein_id": "ENSP00000578288.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 406,
"cds_start": 895,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908229.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.871G>T",
"hgvs_p": "p.Glu291*",
"transcript": "ENST00000908228.1",
"protein_id": "ENSP00000578287.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 398,
"cds_start": 871,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908228.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.871G>T",
"hgvs_p": "p.Glu291*",
"transcript": "ENST00000908243.1",
"protein_id": "ENSP00000578302.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 398,
"cds_start": 871,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908243.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.871G>T",
"hgvs_p": "p.Glu291*",
"transcript": "ENST00000908245.1",
"protein_id": "ENSP00000578304.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 398,
"cds_start": 871,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908245.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.850G>T",
"hgvs_p": "p.Glu284*",
"transcript": "ENST00000908242.1",
"protein_id": "ENSP00000578301.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 391,
"cds_start": 850,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908242.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.844G>T",
"hgvs_p": "p.Glu282*",
"transcript": "ENST00000908230.1",
"protein_id": "ENSP00000578289.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 389,
"cds_start": 844,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908230.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.841G>T",
"hgvs_p": "p.Glu281*",
"transcript": "ENST00000908238.1",
"protein_id": "ENSP00000578297.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 388,
"cds_start": 841,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908238.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.802G>T",
"hgvs_p": "p.Glu268*",
"transcript": "ENST00000908231.1",
"protein_id": "ENSP00000578290.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 375,
"cds_start": 802,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908231.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "ENST00000908241.1",
"protein_id": "ENSP00000578300.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 373,
"cds_start": 853,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908241.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "ENST00000908240.1",
"protein_id": "ENSP00000578299.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 370,
"cds_start": 853,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908240.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*",
"transcript": "ENST00000908237.1",
"protein_id": "ENSP00000578296.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 349,
"cds_start": 853,
"cds_end": null,
"cds_length": 1050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908237.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.697G>T",
"hgvs_p": "p.Glu233*",
"transcript": "ENST00000908227.1",
"protein_id": "ENSP00000578286.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 340,
"cds_start": 697,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908227.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.667G>T",
"hgvs_p": "p.Glu223*",
"transcript": "ENST00000908234.1",
"protein_id": "ENSP00000578293.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 330,
"cds_start": 667,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908234.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGXT",
"gene_hgnc_id": 341,
"hgvs_c": "c.583G>T",
"hgvs_p": "p.Glu195*",
"transcript": "ENST00000908239.1",
"protein_id": "ENSP00000578298.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 302,
"cds_start": 583,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908239.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
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"transcript": "ENST00000908233.1",
"protein_id": "ENSP00000578292.1",
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"aa_start": null,
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"aa_length": 360,
"cds_start": null,
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"biotype": "protein_coding",
"feature": "ENST00000908233.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
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"exon_count": 3,
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"gene_symbol": "AGXT",
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"hgvs_c": "n.631G>T",
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"transcript": "ENST00000470255.1",
"protein_id": null,
"transcript_support_level": 2,
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"cdna_start": null,
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"biotype": "retained_intron",
"feature": "ENST00000470255.1"
}
],
"gene_symbol": "AGXT",
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"dbsnp": "rs180177288",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5299999713897705,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.578,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.13,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000030.3",
"gene_symbol": "AGXT",
"hgnc_id": 341,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.853G>T",
"hgvs_p": "p.Glu285*"
}
],
"clinvar_disease": " type I,Primary hyperoxaluria",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Primary hyperoxaluria, type I",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}