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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: 17-18021850-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=18021850&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 18021850,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000474627.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met",
"transcript": "NM_145691.4",
"protein_id": "NP_663729.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 289,
"cds_start": 511,
"cds_end": null,
"cds_length": 870,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 1553,
"mane_select": "ENST00000474627.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met",
"transcript": "ENST00000474627.8",
"protein_id": "ENSP00000417190.2",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 289,
"cds_start": 511,
"cds_end": null,
"cds_length": 870,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 1553,
"mane_select": "NM_145691.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.*34-612G>A",
"hgvs_p": null,
"transcript": "ENST00000462733.5",
"protein_id": "ENSP00000463920.1",
"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": 1737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met",
"transcript": "ENST00000444058.1",
"protein_id": "ENSP00000397198.1",
"transcript_support_level": 3,
"aa_start": 171,
"aa_end": null,
"aa_length": 204,
"cds_start": 511,
"cds_end": null,
"cds_length": 616,
"cdna_start": 580,
"cdna_end": null,
"cdna_length": 685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met",
"transcript": "XM_011524065.2",
"protein_id": "XP_011522367.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 263,
"cds_start": 511,
"cds_end": null,
"cds_length": 792,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 2089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met",
"transcript": "XM_005256848.5",
"protein_id": "XP_005256905.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 256,
"cds_start": 511,
"cds_end": null,
"cds_length": 771,
"cdna_start": 666,
"cdna_end": null,
"cdna_length": 1246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Val71Met",
"transcript": "XM_017025302.2",
"protein_id": "XP_016880791.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 189,
"cds_start": 211,
"cds_end": null,
"cds_length": 570,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.211G>A",
"hgvs_p": "p.Val71Met",
"transcript": "XM_017025303.1",
"protein_id": "XP_016880792.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 163,
"cds_start": 211,
"cds_end": null,
"cds_length": 492,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1943,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.179G>A",
"hgvs_p": null,
"transcript": "ENST00000469327.5",
"protein_id": null,
"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": 681,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.306G>A",
"hgvs_p": null,
"transcript": "ENST00000488753.1",
"protein_id": null,
"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": 796,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.1016G>A",
"hgvs_p": null,
"transcript": "ENST00000496852.5",
"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": 1662,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.666G>A",
"hgvs_p": null,
"transcript": "XR_007065531.1",
"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": 1106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.*33+2774G>A",
"hgvs_p": null,
"transcript": "ENST00000585101.5",
"protein_id": "ENSP00000463861.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 107,
"cds_start": -4,
"cds_end": null,
"cds_length": 324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "c.47+2774G>A",
"hgvs_p": null,
"transcript": "ENST00000581698.1",
"protein_id": "ENSP00000466008.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": -4,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.*33+2774G>A",
"hgvs_p": null,
"transcript": "ENST00000584205.5",
"protein_id": "ENSP00000462899.1",
"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,
"cdna_end": null,
"cdna_length": 1298,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"hgvs_c": "n.-56G>A",
"hgvs_p": null,
"transcript": "ENST00000465337.2",
"protein_id": null,
"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": 894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATPAF2",
"gene_hgnc_id": 18802,
"dbsnp": "rs62073570",
"frequency_reference_population": 0.008199331,
"hom_count_reference_population": 73,
"allele_count_reference_population": 13233,
"gnomad_exomes_af": 0.00842995,
"gnomad_genomes_af": 0.00598669,
"gnomad_exomes_ac": 12321,
"gnomad_genomes_ac": 912,
"gnomad_exomes_homalt": 64,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006976336240768433,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.364,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2296,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.173,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000474627.8",
"gene_symbol": "ATPAF2",
"hgnc_id": 18802,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.511G>A",
"hgvs_p": "p.Val171Met"
}
],
"clinvar_disease": " nuclear type 1,ATPAF2-related disorder,Mitochondrial complex V (ATP synthase) deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:5 B:3",
"phenotype_combined": "not specified|not provided|Mitochondrial complex V (ATP synthase) deficiency, nuclear type 1|ATPAF2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}