← 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: 19-17555854-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17555854&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COLGALT1",
"hgnc_id": 26182,
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_024656.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.550000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 622,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3647,
"cdna_start": 206,
"cds_end": null,
"cds_length": 1869,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_024656.4",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000252599.9",
"protein_coding": true,
"protein_id": "NP_078932.2",
"strand": true,
"transcript": "NM_024656.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 622,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3647,
"cdna_start": 206,
"cds_end": null,
"cds_length": 1869,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000252599.9",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024656.4",
"protein_coding": true,
"protein_id": "ENSP00000252599.3",
"strand": true,
"transcript": "ENST00000252599.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 688,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3833,
"cdna_start": 192,
"cds_end": null,
"cds_length": 2067,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000886053.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556112.1",
"strand": true,
"transcript": "ENST00000886053.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 680,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3797,
"cdna_start": 183,
"cds_end": null,
"cds_length": 2043,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000886054.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556113.1",
"strand": true,
"transcript": "ENST00000886054.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 650,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2332,
"cdna_start": 221,
"cds_end": null,
"cds_length": 1953,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000886055.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000556114.1",
"strand": true,
"transcript": "ENST00000886055.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 631,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3691,
"cdna_start": 224,
"cds_end": null,
"cds_length": 1896,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000970586.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640645.1",
"strand": true,
"transcript": "ENST00000970586.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 585,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3510,
"cdna_start": 180,
"cds_end": null,
"cds_length": 1758,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000912419.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582478.1",
"strand": true,
"transcript": "ENST00000912419.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 459,
"aa_ref": "S",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1447,
"cdna_start": 206,
"cds_end": null,
"cds_length": 1382,
"cds_start": 141,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000597147.2",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.141G>T",
"hgvs_p": "p.Ser47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468947.2",
"strand": true,
"transcript": "ENST00000597147.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3687,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000690106.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "n.141G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508762.1",
"strand": true,
"transcript": "ENST00000690106.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3691,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000690841.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "n.141G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509464.1",
"strand": true,
"transcript": "ENST00000690841.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3630,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000690947.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "n.141G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510367.1",
"strand": true,
"transcript": "ENST00000690947.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2058,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000692764.1",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "n.54G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000692764.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 539,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3939,
"cdna_start": null,
"cds_end": null,
"cds_length": 1620,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005260080.5",
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"hgvs_c": "c.-682G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005260137.1",
"strand": true,
"transcript": "XM_005260080.5",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1246270631",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000005795892,
"gene_hgnc_id": 26182,
"gene_symbol": "COLGALT1",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000579589,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.335,
"pos": 17555854,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024656.4"
}
]
}