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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: 1-64049707-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=64049707&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 64049707,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_005012.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.180C>T",
"hgvs_p": "p.Leu60Leu",
"transcript": "NM_005012.4",
"protein_id": "NP_005003.2",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 937,
"cds_start": 180,
"cds_end": null,
"cds_length": 2814,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371079.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005012.4"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.180C>T",
"hgvs_p": "p.Leu60Leu",
"transcript": "ENST00000371079.6",
"protein_id": "ENSP00000360120.1",
"transcript_support_level": 1,
"aa_start": 60,
"aa_end": null,
"aa_length": 937,
"cds_start": 180,
"cds_end": null,
"cds_length": 2814,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005012.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371079.6"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.180C>T",
"hgvs_p": "p.Leu60Leu",
"transcript": "ENST00000371080.5",
"protein_id": "ENSP00000360121.1",
"transcript_support_level": 1,
"aa_start": 60,
"aa_end": null,
"aa_length": 393,
"cds_start": 180,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371080.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "XM_011541526.2",
"protein_id": "XP_011539828.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": null,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541526.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "XM_017001377.2",
"protein_id": "XP_016856866.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": null,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001377.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.180C>T",
"hgvs_p": "p.Leu60Leu",
"transcript": "NM_001083592.2",
"protein_id": "NP_001077061.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 393,
"cds_start": 180,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001083592.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.120C>T",
"hgvs_p": "p.Leu40Leu",
"transcript": "XM_017001376.2",
"protein_id": "XP_016856865.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 917,
"cds_start": 120,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001376.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "XM_011541526.2",
"protein_id": "XP_011539828.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": null,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541526.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "XM_017001377.2",
"protein_id": "XP_016856866.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 874,
"cds_start": null,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001377.2"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"hgvs_c": "n.214C>T",
"hgvs_p": null,
"transcript": "ENST00000482426.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000482426.1"
}
],
"gene_symbol": "ROR1",
"gene_hgnc_id": 10256,
"dbsnp": "rs1772626",
"frequency_reference_population": 0.8438474,
"hom_count_reference_population": 576951,
"allele_count_reference_population": 1361433,
"gnomad_exomes_af": 0.848985,
"gnomad_genomes_af": 0.794454,
"gnomad_exomes_ac": 1240676,
"gnomad_genomes_ac": 120757,
"gnomad_exomes_homalt": 528225,
"gnomad_genomes_homalt": 48726,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7699999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.368,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005012.4",
"gene_symbol": "ROR1",
"hgnc_id": 10256,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.180C>T",
"hgvs_p": "p.Leu60Leu"
}
],
"clinvar_disease": " autosomal recessive 108,Hearing loss,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|Hearing loss, autosomal recessive 108",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}