← Back to variant description
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: 1-2406576-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=2406576&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 2406576,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_153818.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.820A>G",
"hgvs_p": "p.Thr274Ala",
"transcript": "NM_002617.4",
"protein_id": "NP_002608.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 326,
"cds_start": 820,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000447513.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002617.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.820A>G",
"hgvs_p": "p.Thr274Ala",
"transcript": "ENST00000447513.7",
"protein_id": "ENSP00000407922.2",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 326,
"cds_start": 820,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002617.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447513.7"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.880A>G",
"hgvs_p": "p.Thr294Ala",
"transcript": "ENST00000288774.8",
"protein_id": "ENSP00000288774.3",
"transcript_support_level": 1,
"aa_start": 294,
"aa_end": null,
"aa_length": 346,
"cds_start": 880,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000288774.8"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.880A>G",
"hgvs_p": "p.Thr294Ala",
"transcript": "NM_153818.2",
"protein_id": "NP_722540.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 346,
"cds_start": 880,
"cds_end": null,
"cds_length": 1041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153818.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.877A>G",
"hgvs_p": "p.Thr293Ala",
"transcript": "NM_001374425.1",
"protein_id": "NP_001361354.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 345,
"cds_start": 877,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374425.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.877A>G",
"hgvs_p": "p.Thr293Ala",
"transcript": "ENST00000874692.1",
"protein_id": "ENSP00000544751.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 345,
"cds_start": 877,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874692.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.820A>G",
"hgvs_p": "p.Thr274Ala",
"transcript": "ENST00000507596.5",
"protein_id": "ENSP00000424291.1",
"transcript_support_level": 5,
"aa_start": 274,
"aa_end": null,
"aa_length": 324,
"cds_start": 820,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507596.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.802A>G",
"hgvs_p": "p.Thr268Ala",
"transcript": "ENST00000874693.1",
"protein_id": "ENSP00000544752.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 320,
"cds_start": 802,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874693.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.445A>G",
"hgvs_p": "p.Thr149Ala",
"transcript": "NM_001374426.1",
"protein_id": "NP_001361355.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 201,
"cds_start": 445,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374426.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.388A>G",
"hgvs_p": "p.Thr130Ala",
"transcript": "NM_001374427.1",
"protein_id": "NP_001361356.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 182,
"cds_start": 388,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374427.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.*186A>G",
"hgvs_p": null,
"transcript": "ENST00000510434.1",
"protein_id": "ENSP00000423051.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000510434.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.772A>G",
"hgvs_p": null,
"transcript": "ENST00000650293.1",
"protein_id": "ENSP00000497980.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650293.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.935A>G",
"hgvs_p": null,
"transcript": "NR_164636.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_164636.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "n.*186A>G",
"hgvs_p": null,
"transcript": "ENST00000510434.1",
"protein_id": "ENSP00000423051.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000510434.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "PEX10",
"gene_hgnc_id": 8851,
"hgvs_c": "c.*286A>G",
"hgvs_p": null,
"transcript": "XM_047422539.1",
"protein_id": "XP_047278495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 209,
"cds_start": null,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422539.1"
}
],
"gene_symbol": "PEX10",
"gene_hgnc_id": 8851,
"dbsnp": "rs34154371",
"frequency_reference_population": 0.02272189,
"hom_count_reference_population": 507,
"allele_count_reference_population": 36655,
"gnomad_exomes_af": 0.0231376,
"gnomad_genomes_af": 0.01873,
"gnomad_exomes_ac": 33805,
"gnomad_genomes_ac": 2850,
"gnomad_exomes_homalt": 465,
"gnomad_genomes_homalt": 42,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010609060525894165,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.357,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1091,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.96,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_153818.2",
"gene_symbol": "PEX10",
"hgnc_id": 8851,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.880A>G",
"hgvs_p": "p.Thr294Ala"
}
],
"clinvar_disease": " complementation group 7,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 6A (Zellweger),Zellweger spectrum disorders,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:5",
"phenotype_combined": "not specified|Peroxisome biogenesis disorder, complementation group 7|Peroxisome biogenesis disorder 6A (Zellweger)|not provided|Zellweger spectrum disorders",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}