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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: 10-121517460-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=121517460&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 121517460,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000358487.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "NM_000141.5",
"protein_id": "NP_000132.3",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 821,
"cds_start": 943,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1576,
"cdna_end": null,
"cdna_length": 4624,
"mane_select": "ENST00000358487.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "ENST00000358487.10",
"protein_id": "ENSP00000351276.6",
"transcript_support_level": 1,
"aa_start": 315,
"aa_end": null,
"aa_length": 821,
"cds_start": 943,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1576,
"cdna_end": null,
"cdna_length": 4624,
"mane_select": "NM_000141.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.676G>T",
"hgvs_p": "p.Ala226Ser",
"transcript": "ENST00000613048.4",
"protein_id": "ENSP00000484154.1",
"transcript_support_level": 5,
"aa_start": 226,
"aa_end": null,
"aa_length": 732,
"cds_start": 676,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 1323,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.598G>T",
"hgvs_p": "p.Ala200Ser",
"transcript": "ENST00000356226.8",
"protein_id": "ENSP00000348559.4",
"transcript_support_level": 1,
"aa_start": 200,
"aa_end": null,
"aa_length": 704,
"cds_start": 598,
"cds_end": null,
"cds_length": 2115,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 3547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.259G>T",
"hgvs_p": "p.Ala87Ser",
"transcript": "ENST00000478859.5",
"protein_id": "ENSP00000474011.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 593,
"cds_start": 259,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 974,
"cdna_end": null,
"cdna_length": 3990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "n.1352G>T",
"hgvs_p": null,
"transcript": "ENST00000490349.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "n.746G>T",
"hgvs_p": null,
"transcript": "ENST00000604236.5",
"protein_id": "ENSP00000474109.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.1087+1222G>T",
"hgvs_p": null,
"transcript": "ENST00000457416.7",
"protein_id": "ENSP00000410294.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 822,
"cds_start": -4,
"cds_end": null,
"cds_length": 2469,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.1087+1222G>T",
"hgvs_p": null,
"transcript": "ENST00000369056.5",
"protein_id": "ENSP00000358052.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 769,
"cds_start": -4,
"cds_end": null,
"cds_length": 2310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.1087+1222G>T",
"hgvs_p": null,
"transcript": "ENST00000369058.7",
"protein_id": "ENSP00000358054.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 767,
"cds_start": -4,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.749-2141G>T",
"hgvs_p": null,
"transcript": "ENST00000369061.8",
"protein_id": "ENSP00000358057.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 709,
"cds_start": -4,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.742+1222G>T",
"hgvs_p": null,
"transcript": "ENST00000369059.5",
"protein_id": "ENSP00000358055.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 707,
"cds_start": -4,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 16,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.939+2519G>T",
"hgvs_p": null,
"transcript": "ENST00000369060.8",
"protein_id": "ENSP00000358056.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 705,
"cds_start": -4,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.820+1222G>T",
"hgvs_p": null,
"transcript": "ENST00000360144.7",
"protein_id": "ENSP00000353262.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 680,
"cds_start": -4,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "NM_001320658.2",
"protein_id": "NP_001307587.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 819,
"cds_start": 943,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1576,
"cdna_end": null,
"cdna_length": 4618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "ENST00000346997.6",
"protein_id": "ENSP00000263451.5",
"transcript_support_level": 5,
"aa_start": 315,
"aa_end": null,
"aa_length": 819,
"cds_start": 943,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 955,
"cdna_end": null,
"cdna_length": 2472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "ENST00000351936.11",
"protein_id": "ENSP00000309878.10",
"transcript_support_level": 5,
"aa_start": 315,
"aa_end": null,
"aa_length": 819,
"cds_start": 943,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1734,
"cdna_end": null,
"cdna_length": 4761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser",
"transcript": "ENST00000683211.1",
"protein_id": "ENSP00000508257.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 819,
"cds_start": 943,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 3937,
"cdna_end": null,
"cdna_length": 6964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.676G>T",
"hgvs_p": "p.Ala226Ser",
"transcript": "NM_023029.3",
"protein_id": "NP_075418.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 732,
"cds_start": 676,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 4357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.676G>T",
"hgvs_p": "p.Ala226Ser",
"transcript": "NM_001441089.1",
"protein_id": "NP_001428018.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 730,
"cds_start": 676,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 4351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.676G>T",
"hgvs_p": "p.Ala226Ser",
"transcript": "NM_001144915.2",
"protein_id": "NP_001138387.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 707,
"cds_start": 676,
"cds_end": null,
"cds_length": 2124,
"cdna_start": 995,
"cdna_end": null,
"cdna_length": 3692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.676G>T",
"hgvs_p": "p.Ala226Ser",
"transcript": "ENST00000357555.9",
"protein_id": "ENSP00000350166.5",
"transcript_support_level": 2,
"aa_start": 226,
"aa_end": null,
"aa_length": 707,
"cds_start": 676,
"cds_end": null,
"cds_length": 2124,
"cdna_start": 995,
"cdna_end": null,
"cdna_length": 3690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"hgvs_c": "c.598G>T",
"hgvs_p": "p.Ala200Ser",
"transcript": "NM_001144916.2",
"protein_id": "NP_001138388.1",
"transcript_support_level": null,
"aa_start": 200,
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{
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{
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},
{
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],
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"transcript": "XM_024447890.2",
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},
{
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],
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"gene_symbol": "FGFR2",
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"hgvs_c": "c.799+1222G>T",
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"transcript": "XM_024447891.2",
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"feature": null
}
],
"gene_symbol": "FGFR2",
"gene_hgnc_id": 3689,
"dbsnp": "rs121918504",
"frequency_reference_population": 0.000006840591,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000684059,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.48647189140319824,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.211,
"revel_prediction": "Benign",
"alphamissense_score": 0.2653,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.851,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PP2,PP5_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 4,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PP2",
"PP5_Very_Strong",
"BS2"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000358487.10",
"gene_symbol": "FGFR2",
"hgnc_id": 3689,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.943G>T",
"hgvs_p": "p.Ala315Ser"
}
],
"clinvar_disease": " nonsyndromic unicoronal,11 conditions,Craniosynostosis,Crouzon syndrome,FGFR2-related craniosynostosis,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "Craniosynostosis, nonsyndromic unicoronal|Crouzon syndrome|not provided|FGFR2-related craniosynostosis|11 conditions",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}