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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: 3-193643409-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193643409&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193643409,
"ref": "A",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000361510.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1342A>C",
"hgvs_p": "p.Arg448Arg",
"transcript": "NM_130837.3",
"protein_id": "NP_570850.2",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1342,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1512,
"cdna_end": null,
"cdna_length": 6429,
"mane_select": "ENST00000361510.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1342A>C",
"hgvs_p": "p.Arg448Arg",
"transcript": "ENST00000361510.8",
"protein_id": "ENSP00000355324.2",
"transcript_support_level": 5,
"aa_start": 448,
"aa_end": null,
"aa_length": 1015,
"cds_start": 1342,
"cds_end": null,
"cds_length": 3048,
"cdna_start": 1512,
"cdna_end": null,
"cdna_length": 6429,
"mane_select": "NM_130837.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1288A>C",
"hgvs_p": "p.Arg430Arg",
"transcript": "ENST00000361908.8",
"protein_id": "ENSP00000354681.3",
"transcript_support_level": 1,
"aa_start": 430,
"aa_end": null,
"aa_length": 997,
"cds_start": 1288,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 6397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1288A>C",
"hgvs_p": "p.Arg430Arg",
"transcript": "NM_130836.3",
"protein_id": "NP_570849.2",
"transcript_support_level": null,
"aa_start": 430,
"aa_end": null,
"aa_length": 997,
"cds_start": 1288,
"cds_end": null,
"cds_length": 2994,
"cdna_start": 1458,
"cdna_end": null,
"cdna_length": 6375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1234A>C",
"hgvs_p": "p.Arg412Arg",
"transcript": "NM_130835.3",
"protein_id": "NP_570848.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 979,
"cds_start": 1234,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 1404,
"cdna_end": null,
"cdna_length": 6321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1234A>C",
"hgvs_p": "p.Arg412Arg",
"transcript": "ENST00000361715.6",
"protein_id": "ENSP00000355311.2",
"transcript_support_level": 5,
"aa_start": 412,
"aa_end": null,
"aa_length": 979,
"cds_start": 1234,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 6384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1231A>C",
"hgvs_p": "p.Arg411Arg",
"transcript": "NM_130834.3",
"protein_id": "NP_570847.2",
"transcript_support_level": null,
"aa_start": 411,
"aa_end": null,
"aa_length": 978,
"cds_start": 1231,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 1401,
"cdna_end": null,
"cdna_length": 6318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1231A>C",
"hgvs_p": "p.Arg411Arg",
"transcript": "ENST00000392437.6",
"protein_id": "ENSP00000376232.2",
"transcript_support_level": 3,
"aa_start": 411,
"aa_end": null,
"aa_length": 978,
"cds_start": 1231,
"cds_end": null,
"cds_length": 2937,
"cdna_start": 1329,
"cdna_end": null,
"cdna_length": 4087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1177A>C",
"hgvs_p": "p.Arg393Arg",
"transcript": "ENST00000392436.7",
"protein_id": "ENSP00000376231.3",
"transcript_support_level": 3,
"aa_start": 393,
"aa_end": null,
"aa_length": 972,
"cds_start": 1177,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 1335,
"cdna_end": null,
"cdna_length": 3579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1192A>C",
"hgvs_p": "p.Arg398Arg",
"transcript": "ENST00000645553.1",
"protein_id": "ENSP00000494725.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 965,
"cds_start": 1192,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 5008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1180A>C",
"hgvs_p": "p.Arg394Arg",
"transcript": "NM_130833.3",
"protein_id": "NP_570846.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 961,
"cds_start": 1180,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1350,
"cdna_end": null,
"cdna_length": 6267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1180A>C",
"hgvs_p": "p.Arg394Arg",
"transcript": "ENST00000361150.6",
"protein_id": "ENSP00000354781.2",
"transcript_support_level": 5,
"aa_start": 394,
"aa_end": null,
"aa_length": 961,
"cds_start": 1180,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1414,
"cdna_end": null,
"cdna_length": 6330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1177A>C",
"hgvs_p": "p.Arg393Arg",
"transcript": "NM_015560.3",
"protein_id": "NP_056375.2",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 960,
"cds_start": 1177,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 6264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1177A>C",
"hgvs_p": "p.Arg393Arg",
"transcript": "ENST00000361828.7",
"protein_id": "ENSP00000354429.3",
"transcript_support_level": 5,
"aa_start": 393,
"aa_end": null,
"aa_length": 960,
"cds_start": 1177,
"cds_end": null,
"cds_length": 2883,
"cdna_start": 1411,
"cdna_end": null,
"cdna_length": 6328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1123A>C",
"hgvs_p": "p.Arg375Arg",
"transcript": "NM_130832.3",
"protein_id": "NP_570845.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 942,
"cds_start": 1123,
"cds_end": null,
"cds_length": 2829,
"cdna_start": 1293,
"cdna_end": null,
"cdna_length": 6210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1069A>C",
"hgvs_p": "p.Arg357Arg",
"transcript": "NM_130831.3",
"protein_id": "NP_570844.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 924,
"cds_start": 1069,
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"cds_length": 2775,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 6156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1069A>C",
"hgvs_p": "p.Arg357Arg",
"transcript": "ENST00000646793.1",
"protein_id": "ENSP00000494512.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 924,
"cds_start": 1069,
"cds_end": null,
"cds_length": 2775,
"cdna_start": 1200,
"cdna_end": null,
"cdna_length": 5830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.859A>C",
"hgvs_p": "p.Arg287Arg",
"transcript": "ENST00000643329.1",
"protein_id": "ENSP00000493673.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 854,
"cds_start": 859,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 6068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.808A>C",
"hgvs_p": "p.Arg270Arg",
"transcript": "NM_001354663.2",
"protein_id": "NP_001341592.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 837,
"cds_start": 808,
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"cdna_start": 1408,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.805A>C",
"hgvs_p": "p.Arg269Arg",
"transcript": "NM_001354664.2",
"protein_id": "NP_001341593.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 836,
"cds_start": 805,
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"cdna_start": 1405,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.163A>C",
"hgvs_p": "p.Arg55Arg",
"transcript": "ENST00000646544.1",
"protein_id": "ENSP00000495028.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 622,
"cds_start": 163,
"cds_end": null,
"cds_length": 1869,
"cdna_start": 165,
"cdna_end": null,
"cdna_length": 5071,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1342A>C",
"hgvs_p": "p.Arg448Arg",
"transcript": "XM_047448206.1",
"protein_id": "XP_047304162.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 1047,
"cds_start": 1342,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 1512,
"cdna_end": null,
"cdna_length": 3338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.1288A>C",
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"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "n.*605A>C",
"hgvs_p": null,
"transcript": "ENST00000646699.1",
"protein_id": "ENSP00000493913.1",
"transcript_support_level": null,
"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": 3943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"dbsnp": "rs149752576",
"frequency_reference_population": 0.0041531175,
"hom_count_reference_population": 86,
"allele_count_reference_population": 6695,
"gnomad_exomes_af": 0.00426528,
"gnomad_genomes_af": 0.00307844,
"gnomad_exomes_ac": 6226,
"gnomad_genomes_ac": 469,
"gnomad_exomes_homalt": 83,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.096,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.06,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000361510.8",
"gene_symbol": "OPA1",
"hgnc_id": 8140,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.1342A>C",
"hgvs_p": "p.Arg448Arg"
}
],
"clinvar_disease": "Autosomal dominant optic atrophy classic form,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|not provided|Autosomal dominant optic atrophy classic form",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}