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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: 14-50628186-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=50628186&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 50628186,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000358385.12",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "NM_015915.5",
"protein_id": "NP_056999.2",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 558,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 2504,
"mane_select": "ENST00000358385.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000358385.12",
"protein_id": "ENSP00000351155.7",
"transcript_support_level": 1,
"aa_start": 425,
"aa_end": null,
"aa_length": 558,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 2504,
"mane_select": "NM_015915.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000441560.6",
"protein_id": "ENSP00000413675.2",
"transcript_support_level": 1,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1756,
"cdna_end": null,
"cdna_length": 2853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000682037.1",
"protein_id": "ENSP00000508289.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 619,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1609,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "NM_001127713.1",
"protein_id": "NP_001121185.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1700,
"cdna_end": null,
"cdna_length": 2816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "NM_181598.4",
"protein_id": "NP_853629.2",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000553509.2",
"protein_id": "ENSP00000450989.2",
"transcript_support_level": 4,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1713,
"cdna_end": null,
"cdna_length": 3778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000556478.3",
"protein_id": "ENSP00000501428.2",
"transcript_support_level": 2,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1779,
"cdna_end": null,
"cdna_length": 3844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "ENST00000713928.1",
"protein_id": "ENSP00000519225.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 553,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1565,
"cdna_end": null,
"cdna_length": 2673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1218A>G",
"hgvs_p": "p.Ile406Met",
"transcript": "ENST00000713929.1",
"protein_id": "ENSP00000519226.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 534,
"cds_start": 1218,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 1337,
"cdna_end": null,
"cdna_length": 2058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1026A>G",
"hgvs_p": "p.Ile342Met",
"transcript": "ENST00000557735.2",
"protein_id": "ENSP00000451015.2",
"transcript_support_level": 4,
"aa_start": 342,
"aa_end": null,
"aa_length": 470,
"cds_start": 1026,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1455,
"cdna_end": null,
"cdna_length": 2106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1026A>G",
"hgvs_p": "p.Ile342Met",
"transcript": "ENST00000674503.2",
"protein_id": "ENSP00000501520.2",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 470,
"cds_start": 1026,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1421,
"cdna_end": null,
"cdna_length": 2235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1026A>G",
"hgvs_p": "p.Ile342Met",
"transcript": "ENST00000713930.1",
"protein_id": "ENSP00000519227.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 470,
"cds_start": 1026,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1372,
"cdna_end": null,
"cdna_length": 3437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1026A>G",
"hgvs_p": "p.Ile342Met",
"transcript": "ENST00000713931.1",
"protein_id": "ENSP00000519228.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 470,
"cds_start": 1026,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1338,
"cdna_end": null,
"cdna_length": 1990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met",
"transcript": "XM_047431430.1",
"protein_id": "XP_047287386.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 558,
"cds_start": 1275,
"cds_end": null,
"cds_length": 1677,
"cdna_start": 1700,
"cdna_end": null,
"cdna_length": 2831,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.21A>G",
"hgvs_p": null,
"transcript": "ENST00000556067.1",
"protein_id": "ENSP00000451100.1",
"transcript_support_level": 4,
"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": 550,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.*2567A>G",
"hgvs_p": null,
"transcript": "ENST00000674288.1",
"protein_id": "ENSP00000501522.1",
"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": 5298,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.2613A>G",
"hgvs_p": null,
"transcript": "ENST00000682219.1",
"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": 3321,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.1196A>G",
"hgvs_p": null,
"transcript": "ENST00000683037.1",
"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": 1900,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.1609A>G",
"hgvs_p": null,
"transcript": "ENST00000683330.1",
"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": 2976,
"mane_select": null,
"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": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.*2567A>G",
"hgvs_p": null,
"transcript": "ENST00000674288.1",
"protein_id": "ENSP00000501522.1",
"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": 5298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"hgvs_c": "n.*259A>G",
"hgvs_p": null,
"transcript": "ENST00000555266.1",
"protein_id": "ENSP00000450897.1",
"transcript_support_level": 3,
"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": 383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATL1",
"gene_hgnc_id": 11231,
"dbsnp": "rs1273371448",
"frequency_reference_population": 0.000003717251,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000205215,
"gnomad_genomes_af": 0.0000197094,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5963773727416992,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.214,
"revel_prediction": "Benign",
"alphamissense_score": 0.0976,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.069,
"phylop100way_prediction": "Benign",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000358385.12",
"gene_symbol": "ATL1",
"hgnc_id": 11231,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,SD",
"hgvs_c": "c.1275A>G",
"hgvs_p": "p.Ile425Met"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 3A",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary spastic paraplegia 3A",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}