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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: 3-15488236-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=15488236&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COLQ",
"hgnc_id": 2226,
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_005677.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -7,
"allele_count_reference_population": 59,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"chr": "3",
"clinvar_classification": "Likely benign",
"clinvar_disease": "COLQ-related disorder,Congenital myasthenic syndrome 5",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5899999737739563,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 455,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2960,
"cdna_start": 372,
"cds_end": null,
"cds_length": 1368,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_005677.4",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000383788.10",
"protein_coding": true,
"protein_id": "NP_005668.2",
"strand": false,
"transcript": "NM_005677.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 455,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2960,
"cdna_start": 372,
"cds_end": null,
"cds_length": 1368,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000383788.10",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005677.4",
"protein_coding": true,
"protein_id": "ENSP00000373298.3",
"strand": false,
"transcript": "ENST00000383788.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 456,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1668,
"cdna_start": 417,
"cds_end": null,
"cds_length": 1371,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000603808.5",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474271.1",
"strand": false,
"transcript": "ENST00000603808.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 460,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3066,
"cdna_start": 463,
"cds_end": null,
"cds_length": 1383,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874202.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544261.1",
"strand": false,
"transcript": "ENST00000874202.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 455,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2924,
"cdna_start": 368,
"cds_end": null,
"cds_length": 1368,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 18,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000959102.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629161.1",
"strand": false,
"transcript": "ENST00000959102.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 448,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2937,
"cdna_start": 373,
"cds_end": null,
"cds_length": 1347,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959107.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629166.1",
"strand": false,
"transcript": "ENST00000959107.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 446,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2989,
"cdna_start": 427,
"cds_end": null,
"cds_length": 1341,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874203.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544262.1",
"strand": false,
"transcript": "ENST00000874203.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 445,
"aa_ref": "S",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3134,
"cdna_start": 546,
"cds_end": null,
"cds_length": 1338,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_080538.2",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.261G>T",
"hgvs_p": "p.Ser87Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_536799.1",
"strand": false,
"transcript": "NM_080538.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 445,
"aa_ref": "S",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2784,
"cdna_start": 546,
"cds_end": null,
"cds_length": 1338,
"cds_start": 261,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000383781.8",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.261G>T",
"hgvs_p": "p.Ser87Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373291.3",
"strand": false,
"transcript": "ENST00000383781.8",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 439,
"aa_ref": "S",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2909,
"cdna_start": 370,
"cds_end": null,
"cds_length": 1320,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874205.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544264.1",
"strand": false,
"transcript": "ENST00000874205.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 422,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2870,
"cdna_start": 386,
"cds_end": null,
"cds_length": 1269,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000874204.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544263.1",
"strand": false,
"transcript": "ENST00000874204.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
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"aa_length": 401,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2806,
"cdna_start": 382,
"cds_end": null,
"cds_length": 1206,
"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959106.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629165.1",
"strand": false,
"transcript": "ENST00000959106.1",
"transcript_support_level": null
},
{
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"aa_length": 328,
"aa_ref": "S",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2612,
"cdna_start": 406,
"cds_end": null,
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"cds_start": 291,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
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"feature": "ENST00000959104.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.291G>T",
"hgvs_p": "p.Ser97Ser",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629163.1",
"strand": false,
"transcript": "ENST00000959104.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": 421,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2858,
"cdna_start": null,
"cds_end": null,
"cds_length": 1266,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_080539.4",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.219+1289G>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_536800.2",
"strand": false,
"transcript": "NM_080539.4",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
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"cds_start": null,
"consequences": [
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],
"exon_count": 16,
"exon_rank": null,
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"feature": "ENST00000383786.9",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.219+1289G>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373296.3",
"strand": false,
"transcript": "ENST00000383786.9",
"transcript_support_level": 5
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2788,
"cdna_start": null,
"cds_end": null,
"cds_length": 1167,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959105.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.219+1289G>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629164.1",
"strand": false,
"transcript": "ENST00000959105.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2813,
"cdna_start": null,
"cds_end": null,
"cds_length": 1137,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000959103.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.219+1289G>T",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629162.1",
"strand": false,
"transcript": "ENST00000959103.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_end": null,
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"cds_start": null,
"consequences": [
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],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000605797.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "c.150+1289G>T",
"hgvs_p": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474936.1",
"strand": false,
"transcript": "ENST00000605797.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
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"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000679838.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.*53G>T",
"hgvs_p": null,
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505708.1",
"strand": false,
"transcript": "ENST00000679838.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2783,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000681097.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.291G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505397.1",
"strand": false,
"transcript": "ENST00000681097.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2947,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000679838.1",
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"hgvs_c": "n.*53G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505708.1",
"strand": false,
"transcript": "ENST00000679838.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
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"dbsnp": "rs115201284",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000036575402,
"gene_hgnc_id": 2226,
"gene_symbol": "COLQ",
"gnomad_exomes_ac": 38,
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"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Congenital myasthenic syndrome 5|COLQ-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -6.992,
"pos": 15488236,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.12999999523162842,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.13,
"transcript": "NM_005677.4"
}
]
}