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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: 12-88049227-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88049227&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 88049227,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_025114.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7397T>C",
"hgvs_p": "p.Phe2466Ser",
"transcript": "NM_025114.4",
"protein_id": "NP_079390.3",
"transcript_support_level": null,
"aa_start": 2466,
"aa_end": null,
"aa_length": 2479,
"cds_start": 7397,
"cds_end": null,
"cds_length": 7440,
"cdna_start": 7613,
"cdna_end": null,
"cdna_length": 7824,
"mane_select": "ENST00000552810.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 54,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7397T>C",
"hgvs_p": "p.Phe2466Ser",
"transcript": "ENST00000552810.6",
"protein_id": "ENSP00000448012.1",
"transcript_support_level": 1,
"aa_start": 2466,
"aa_end": null,
"aa_length": 2479,
"cds_start": 7397,
"cds_end": null,
"cds_length": 7440,
"cdna_start": 7613,
"cdna_end": null,
"cdna_length": 7824,
"mane_select": "NM_025114.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4364T>C",
"hgvs_p": "p.Phe1455Ser",
"transcript": "ENST00000547691.8",
"protein_id": "ENSP00000446905.3",
"transcript_support_level": 1,
"aa_start": 1455,
"aa_end": null,
"aa_length": 1468,
"cds_start": 4364,
"cds_end": null,
"cds_length": 4407,
"cdna_start": 4366,
"cdna_end": null,
"cdna_length": 4577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RLIG1",
"gene_hgnc_id": 25322,
"hgvs_c": "n.*1548A>G",
"hgvs_p": null,
"transcript": "ENST00000550333.5",
"protein_id": "ENSP00000448194.1",
"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": 2740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RLIG1",
"gene_hgnc_id": 25322,
"hgvs_c": "c.*805A>G",
"hgvs_p": null,
"transcript": "NM_001009894.3",
"protein_id": "NP_001009894.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2829,
"mane_select": "ENST00000356891.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RLIG1",
"gene_hgnc_id": 25322,
"hgvs_c": "c.*805A>G",
"hgvs_p": null,
"transcript": "ENST00000356891.4",
"protein_id": "ENSP00000349358.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2829,
"mane_select": "NM_001009894.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RLIG1",
"gene_hgnc_id": 25322,
"hgvs_c": "n.*1548A>G",
"hgvs_p": null,
"transcript": "ENST00000550333.5",
"protein_id": "ENSP00000448194.1",
"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": 2740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8258T>C",
"hgvs_p": "p.Phe2753Ser",
"transcript": "ENST00000675476.1",
"protein_id": "ENSP00000502161.1",
"transcript_support_level": null,
"aa_start": 2753,
"aa_end": null,
"aa_length": 2766,
"cds_start": 8258,
"cds_end": null,
"cds_length": 8301,
"cdna_start": 8485,
"cdna_end": null,
"cdna_length": 8696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8165T>C",
"hgvs_p": "p.Phe2722Ser",
"transcript": "ENST00000675833.1",
"protein_id": "ENSP00000502559.1",
"transcript_support_level": null,
"aa_start": 2722,
"aa_end": null,
"aa_length": 2735,
"cds_start": 8165,
"cds_end": null,
"cds_length": 8208,
"cdna_start": 8392,
"cdna_end": null,
"cdna_length": 8603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7406T>C",
"hgvs_p": "p.Phe2469Ser",
"transcript": "ENST00000309041.12",
"protein_id": "ENSP00000308021.8",
"transcript_support_level": 5,
"aa_start": 2469,
"aa_end": null,
"aa_length": 2482,
"cds_start": 7406,
"cds_end": null,
"cds_length": 7449,
"cdna_start": 7633,
"cdna_end": null,
"cdna_length": 7844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7376T>C",
"hgvs_p": "p.Phe2459Ser",
"transcript": "ENST00000675230.1",
"protein_id": "ENSP00000502503.1",
"transcript_support_level": null,
"aa_start": 2459,
"aa_end": null,
"aa_length": 2472,
"cds_start": 7376,
"cds_end": null,
"cds_length": 7419,
"cdna_start": 7603,
"cdna_end": null,
"cdna_length": 7814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7274T>C",
"hgvs_p": "p.Phe2425Ser",
"transcript": "ENST00000673058.2",
"protein_id": "ENSP00000500665.2",
"transcript_support_level": null,
"aa_start": 2425,
"aa_end": null,
"aa_length": 2438,
"cds_start": 7274,
"cds_end": null,
"cds_length": 7317,
"cdna_start": 7501,
"cdna_end": null,
"cdna_length": 7712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 53,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7232T>C",
"hgvs_p": "p.Phe2411Ser",
"transcript": "ENST00000675408.1",
"protein_id": "ENSP00000502298.1",
"transcript_support_level": null,
"aa_start": 2411,
"aa_end": null,
"aa_length": 2424,
"cds_start": 7232,
"cds_end": null,
"cds_length": 7275,
"cdna_start": 7459,
"cdna_end": null,
"cdna_length": 7670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8267T>C",
"hgvs_p": "p.Phe2756Ser",
"transcript": "XM_011538756.4",
"protein_id": "XP_011537058.1",
"transcript_support_level": null,
"aa_start": 2756,
"aa_end": null,
"aa_length": 2769,
"cds_start": 8267,
"cds_end": null,
"cds_length": 8310,
"cdna_start": 8483,
"cdna_end": null,
"cdna_length": 8694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8267T>C",
"hgvs_p": "p.Phe2756Ser",
"transcript": "XM_011538757.4",
"protein_id": "XP_011537059.1",
"transcript_support_level": null,
"aa_start": 2756,
"aa_end": null,
"aa_length": 2769,
"cds_start": 8267,
"cds_end": null,
"cds_length": 8310,
"cdna_start": 8421,
"cdna_end": null,
"cdna_length": 8632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8264T>C",
"hgvs_p": "p.Phe2755Ser",
"transcript": "XM_011538758.4",
"protein_id": "XP_011537060.1",
"transcript_support_level": null,
"aa_start": 2755,
"aa_end": null,
"aa_length": 2768,
"cds_start": 8264,
"cds_end": null,
"cds_length": 8307,
"cdna_start": 8480,
"cdna_end": null,
"cdna_length": 8691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8258T>C",
"hgvs_p": "p.Phe2753Ser",
"transcript": "XM_011538759.3",
"protein_id": "XP_011537061.1",
"transcript_support_level": null,
"aa_start": 2753,
"aa_end": null,
"aa_length": 2766,
"cds_start": 8258,
"cds_end": null,
"cds_length": 8301,
"cdna_start": 8474,
"cdna_end": null,
"cdna_length": 8685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8144T>C",
"hgvs_p": "p.Phe2715Ser",
"transcript": "XM_011538760.3",
"protein_id": "XP_011537062.1",
"transcript_support_level": null,
"aa_start": 2715,
"aa_end": null,
"aa_length": 2728,
"cds_start": 8144,
"cds_end": null,
"cds_length": 8187,
"cdna_start": 8360,
"cdna_end": null,
"cdna_length": 8571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8135T>C",
"hgvs_p": "p.Phe2712Ser",
"transcript": "XM_017019980.3",
"protein_id": "XP_016875469.1",
"transcript_support_level": null,
"aa_start": 2712,
"aa_end": null,
"aa_length": 2725,
"cds_start": 8135,
"cds_end": null,
"cds_length": 8178,
"cdna_start": 8351,
"cdna_end": null,
"cdna_length": 8562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8102T>C",
"hgvs_p": "p.Phe2701Ser",
"transcript": "XM_011538761.3",
"protein_id": "XP_011537063.1",
"transcript_support_level": null,
"aa_start": 2701,
"aa_end": null,
"aa_length": 2714,
"cds_start": 8102,
"cds_end": null,
"cds_length": 8145,
"cdna_start": 8318,
"cdna_end": null,
"cdna_length": 8529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.8093T>C",
"hgvs_p": "p.Phe2698Ser",
"transcript": "XM_017019981.3",
"protein_id": "XP_016875470.1",
"transcript_support_level": null,
"aa_start": 2698,
"aa_end": null,
"aa_length": 2711,
"cds_start": 8093,
"cds_end": null,
"cds_length": 8136,
"cdna_start": 8309,
"cdna_end": null,
"cdna_length": 8520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.7499T>C",
"hgvs_p": "p.Phe2500Ser",
"transcript": "XM_011538762.4",
"protein_id": "XP_011537064.1",
"transcript_support_level": null,
"aa_start": 2500,
"aa_end": null,
"aa_length": 2513,
"cds_start": 7499,
"cds_end": null,
"cds_length": 7542,
"cdna_start": 7715,
"cdna_end": null,
"cdna_length": 7926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
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"intron_rank_end": null,
"gene_symbol": "RLIG1",
"gene_hgnc_id": 25322,
"hgvs_c": "n.*1350A>G",
"hgvs_p": null,
"transcript": "ENST00000552121.5",
"protein_id": "ENSP00000447327.1",
"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": 1578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"dbsnp": "rs1159836808",
"frequency_reference_population": 0.000005609273,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.0000048192,
"gnomad_genomes_af": 0.000013161,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02574583888053894,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0645,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.498,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_025114.4",
"gene_symbol": "CEP290",
"hgnc_id": 29021,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7397T>C",
"hgvs_p": "p.Phe2466Ser"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001009894.3",
"gene_symbol": "RLIG1",
"hgnc_id": 25322,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*805A>G",
"hgvs_p": null
}
],
"clinvar_disease": "CEP290-related disorder,Joubert syndrome,Leber congenital amaurosis,Meckel-Gruber syndrome,Nephronophthisis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis|Leber congenital amaurosis|CEP290-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}