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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: 16-1519960-TCTTGGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1519960&ref=TCTTGGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1519960,
"ref": "TCTTGGC",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000426508.7",
"consequences": [
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "NM_014714.4",
"protein_id": "NP_055529.2",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4286,
"cdna_end": null,
"cdna_length": 5232,
"mane_select": "ENST00000426508.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "ENST00000426508.7",
"protein_id": "ENSP00000406012.2",
"transcript_support_level": 5,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4286,
"cdna_end": null,
"cdna_length": 5232,
"mane_select": "NM_014714.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.1537_1542delGCCAAG",
"hgvs_p": "p.Ala513_Lys514del",
"transcript": "ENST00000361339.9",
"protein_id": "ENSP00000354895.5",
"transcript_support_level": 1,
"aa_start": 513,
"aa_end": null,
"aa_length": 656,
"cds_start": 1537,
"cds_end": null,
"cds_length": 1971,
"cdna_start": 2041,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.73_78delGCCAAG",
"hgvs_p": "p.Ala25_Lys26del",
"transcript": "ENST00000568837.1",
"protein_id": "ENSP00000458439.1",
"transcript_support_level": 3,
"aa_start": 25,
"aa_end": null,
"aa_length": 125,
"cds_start": 73,
"cds_end": null,
"cds_length": 378,
"cdna_start": 78,
"cdna_end": null,
"cdna_length": 414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_006720990.4",
"protein_id": "XP_006721053.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4276,
"cdna_end": null,
"cdna_length": 5222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_006720991.4",
"protein_id": "XP_006721054.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 5292,
"cdna_end": null,
"cdna_length": 6238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_047434965.1",
"protein_id": "XP_047290921.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4029,
"cdna_end": null,
"cdna_length": 4975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_047434966.1",
"protein_id": "XP_047290922.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4842,
"cdna_end": null,
"cdna_length": 5788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_047434967.1",
"protein_id": "XP_047290923.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 5418,
"cdna_end": null,
"cdna_length": 6364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_047434968.1",
"protein_id": "XP_047290924.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 5429,
"cdna_end": null,
"cdna_length": 6375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del",
"transcript": "XM_047434969.1",
"protein_id": "XP_047290925.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1462,
"cds_start": 3955,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 4745,
"cdna_end": null,
"cdna_length": 5691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.3709_3714delGCCAAG",
"hgvs_p": "p.Ala1237_Lys1238del",
"transcript": "XM_047434970.1",
"protein_id": "XP_047290926.1",
"transcript_support_level": null,
"aa_start": 1237,
"aa_end": null,
"aa_length": 1380,
"cds_start": 3709,
"cds_end": null,
"cds_length": 4143,
"cdna_start": 4040,
"cdna_end": null,
"cdna_length": 4986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.2980_2985delGCCAAG",
"hgvs_p": "p.Ala994_Lys995del",
"transcript": "XM_011522767.2",
"protein_id": "XP_011521069.1",
"transcript_support_level": null,
"aa_start": 994,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2980,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 3042,
"cdna_end": null,
"cdna_length": 3988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.2140_2145delGCCAAG",
"hgvs_p": "p.Ala714_Lys715del",
"transcript": "XM_047434971.1",
"protein_id": "XP_047290927.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 857,
"cds_start": 2140,
"cds_end": null,
"cds_length": 2574,
"cdna_start": 2281,
"cdna_end": null,
"cdna_length": 3227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "AK",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.1588_1593delGCCAAG",
"hgvs_p": "p.Ala530_Lys531del",
"transcript": "XM_006720992.4",
"protein_id": "XP_006721055.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 673,
"cds_start": 1588,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 4800,
"cdna_end": null,
"cdna_length": 5746,
"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": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "n.*2393_*2398delGCCAAG",
"hgvs_p": null,
"transcript": "ENST00000397417.6",
"protein_id": "ENSP00000380562.2",
"transcript_support_level": 5,
"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": 4023,
"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": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "n.3779_3784delGCCAAG",
"hgvs_p": null,
"transcript": "ENST00000565298.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 4727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "n.*2393_*2398delGCCAAG",
"hgvs_p": null,
"transcript": "ENST00000397417.6",
"protein_id": "ENSP00000380562.2",
"transcript_support_level": 5,
"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": 4023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"dbsnp": "rs746697405",
"frequency_reference_population": 0.0020465155,
"hom_count_reference_population": 8,
"allele_count_reference_population": 3289,
"gnomad_exomes_af": 0.00212131,
"gnomad_genomes_af": 0.00133235,
"gnomad_exomes_ac": 3086,
"gnomad_genomes_ac": 203,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.369,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP3,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000426508.7",
"gene_symbol": "IFT140",
"hgnc_id": 29077,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3955_3960delGCCAAG",
"hgvs_p": "p.Ala1319_Lys1320del"
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 1,IFT140-related disorder,Inborn genetic diseases,Orofacial-digital syndrome III,Retinal dystrophy,Saldino-Mainzer syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 B:1",
"phenotype_combined": "Asphyxiating thoracic dystrophy 1;Orofacial-digital syndrome III|Saldino-Mainzer syndrome|not provided|Retinal dystrophy|not specified|Inborn genetic diseases|IFT140-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}