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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: 2-46950389-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=46950389&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 46950389,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000319190.11",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "NM_020458.4",
"protein_id": "NP_065191.2",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 858,
"cds_start": 211,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 5095,
"mane_select": "ENST00000319190.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "ENST00000319190.11",
"protein_id": "ENSP00000316699.5",
"transcript_support_level": 2,
"aa_start": 71,
"aa_end": null,
"aa_length": 858,
"cds_start": 211,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 5095,
"mane_select": "NM_020458.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "ENST00000394850.6",
"protein_id": "ENSP00000378320.2",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 882,
"cds_start": 211,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 467,
"cdna_end": null,
"cdna_length": 4306,
"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": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.208G>A",
"hgvs_p": null,
"transcript": "ENST00000441914.5",
"protein_id": "ENSP00000393022.1",
"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": 2418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "NM_001288951.2",
"protein_id": "NP_001275880.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 882,
"cds_start": 211,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 5167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Glu37Lys",
"transcript": "NM_001288953.2",
"protein_id": "NP_001275882.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 824,
"cds_start": 109,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 5399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.109G>A",
"hgvs_p": "p.Glu37Lys",
"transcript": "ENST00000409245.5",
"protein_id": "ENSP00000386307.1",
"transcript_support_level": 2,
"aa_start": 37,
"aa_end": null,
"aa_length": 824,
"cds_start": 109,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 542,
"cdna_end": null,
"cdna_length": 3033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_017004524.2",
"protein_id": "XP_016860013.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 819,
"cds_start": 211,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Glu15Lys",
"transcript": "XM_017004525.2",
"protein_id": "XP_016860014.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 802,
"cds_start": 43,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 5431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_017004526.2",
"protein_id": "XP_016860015.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 775,
"cds_start": 211,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 4846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_047445146.1",
"protein_id": "XP_047301102.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 736,
"cds_start": 211,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 4729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_011532999.3",
"protein_id": "XP_011531301.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 681,
"cds_start": 211,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 3242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_047445147.1",
"protein_id": "XP_047301103.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 632,
"cds_start": 211,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 2641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_047445149.1",
"protein_id": "XP_047301105.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 620,
"cds_start": 211,
"cds_end": null,
"cds_length": 1863,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 2247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys",
"transcript": "XM_047445150.1",
"protein_id": "XP_047301106.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 466,
"cds_start": 211,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 1810,
"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": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.211G>A",
"hgvs_p": null,
"transcript": "ENST00000461601.5",
"protein_id": "ENSP00000513496.1",
"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,
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"cdna_length": 2204,
"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": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.830G>A",
"hgvs_p": null,
"transcript": "ENST00000698500.1",
"protein_id": null,
"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": 6587,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.532G>A",
"hgvs_p": null,
"transcript": "ENST00000698501.1",
"protein_id": null,
"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": 1353,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.192G>A",
"hgvs_p": null,
"transcript": "ENST00000698502.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 772,
"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": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.529G>A",
"hgvs_p": null,
"transcript": "XR_007078570.1",
"protein_id": null,
"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": 2670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.-694G>A",
"hgvs_p": null,
"transcript": "NM_001288955.2",
"protein_id": "NP_001275884.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 504,
"cds_start": -4,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "c.-54G>A",
"hgvs_p": null,
"transcript": "XM_047445148.1",
"protein_id": "XP_047301104.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 770,
"cds_start": -4,
"cds_end": null,
"cds_length": 2313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"hgvs_c": "n.-33G>A",
"hgvs_p": null,
"transcript": "ENST00000409825.5",
"protein_id": "ENSP00000386521.1",
"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": 4739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TTC7A",
"gene_hgnc_id": 19750,
"dbsnp": "rs147914967",
"frequency_reference_population": 0.00005390321,
"hom_count_reference_population": 0,
"allele_count_reference_population": 87,
"gnomad_exomes_af": 0.0000560932,
"gnomad_genomes_af": 0.0000328623,
"gnomad_exomes_ac": 82,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9059529304504395,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.795,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9339,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.151,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000319190.11",
"gene_symbol": "TTC7A",
"hgnc_id": 19750,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Glu71Lys"
}
],
"clinvar_disease": "Gastrointestinal defect and immunodeficiency syndrome,Gastrointestinal defects and immunodeficiency syndrome 1,Multiple gastrointestinal atresias,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1 US:1",
"phenotype_combined": "Multiple gastrointestinal atresias|Gastrointestinal defect and immunodeficiency syndrome|Gastrointestinal defects and immunodeficiency syndrome 1|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}