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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: 19-17555733-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17555733&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17555733,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_024656.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "NM_024656.4",
"protein_id": "NP_078932.2",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 622,
"cds_start": 20,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000252599.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024656.4"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000252599.9",
"protein_id": "ENSP00000252599.3",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 622,
"cds_start": 20,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024656.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252599.9"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000886053.1",
"protein_id": "ENSP00000556112.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 688,
"cds_start": 20,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886053.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000886054.1",
"protein_id": "ENSP00000556113.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 680,
"cds_start": 20,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886054.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000886055.1",
"protein_id": "ENSP00000556114.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 650,
"cds_start": 20,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886055.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000970586.1",
"protein_id": "ENSP00000640645.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 631,
"cds_start": 20,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970586.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000912419.1",
"protein_id": "ENSP00000582478.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 585,
"cds_start": 20,
"cds_end": null,
"cds_length": 1758,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912419.1"
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly",
"transcript": "ENST00000597147.2",
"protein_id": "ENSP00000468947.2",
"transcript_support_level": 5,
"aa_start": 7,
"aa_end": null,
"aa_length": 459,
"cds_start": 20,
"cds_end": null,
"cds_length": 1382,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000597147.2"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "n.20C>G",
"hgvs_p": null,
"transcript": "ENST00000690106.1",
"protein_id": "ENSP00000508762.1",
"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": "ENST00000690106.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "n.20C>G",
"hgvs_p": null,
"transcript": "ENST00000690841.1",
"protein_id": "ENSP00000509464.1",
"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": "ENST00000690841.1"
},
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "n.20C>G",
"hgvs_p": null,
"transcript": "ENST00000690947.1",
"protein_id": "ENSP00000510367.1",
"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": "ENST00000690947.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "c.-803C>G",
"hgvs_p": null,
"transcript": "XM_005260080.5",
"protein_id": "XP_005260137.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": null,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005260080.5"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NIBAN3",
"gene_hgnc_id": 24130,
"hgvs_c": "c.*574C>G",
"hgvs_p": null,
"transcript": "XM_011527786.3",
"protein_id": "XP_011526088.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": null,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527786.3"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"hgvs_c": "n.-68C>G",
"hgvs_p": null,
"transcript": "ENST00000692764.1",
"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": "retained_intron",
"feature": "ENST00000692764.1"
}
],
"gene_symbol": "COLGALT1",
"gene_hgnc_id": 26182,
"dbsnp": "rs1449330996",
"frequency_reference_population": 0.0000033318563,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000190608,
"gnomad_genomes_af": 0.0000132226,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0698491632938385,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.213,
"revel_prediction": "Benign",
"alphamissense_score": 0.0575,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.056,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024656.4",
"gene_symbol": "COLGALT1",
"hgnc_id": 26182,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.20C>G",
"hgvs_p": "p.Ala7Gly"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XM_011527786.3",
"gene_symbol": "NIBAN3",
"hgnc_id": 24130,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*574C>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}