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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: 2-69938229-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=69938229&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MXD1",
"hgnc_id": 6761,
"hgvs_c": "c.611C>T",
"hgvs_p": "p.Thr204Ile",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_002357.4",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ASPRV1",
"hgnc_id": 26321,
"hgvs_c": "n.1101-5036G>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NR_170375.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 367,
"alphamissense_prediction": null,
"alphamissense_score": 0.1266,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.12696751952171326,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 221,
"aa_ref": "T",
"aa_start": 204,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5549,
"cdna_start": 833,
"cds_end": null,
"cds_length": 666,
"cds_start": 611,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_002357.4",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.611C>T",
"hgvs_p": "p.Thr204Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264444.7",
"protein_coding": true,
"protein_id": "NP_002348.1",
"strand": true,
"transcript": "NM_002357.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 221,
"aa_ref": "T",
"aa_start": 204,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5549,
"cdna_start": 833,
"cds_end": null,
"cds_length": 666,
"cds_start": 611,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000264444.7",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.611C>T",
"hgvs_p": "p.Thr204Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002357.4",
"protein_coding": true,
"protein_id": "ENSP00000264444.2",
"strand": true,
"transcript": "ENST00000264444.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 211,
"aa_ref": "T",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5580,
"cdna_start": 871,
"cds_end": null,
"cds_length": 636,
"cds_start": 581,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000540449.5",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.581C>T",
"hgvs_p": "p.Thr194Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443935.1",
"strand": true,
"transcript": "ENST00000540449.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 220,
"aa_ref": "T",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5546,
"cdna_start": 830,
"cds_end": null,
"cds_length": 663,
"cds_start": 608,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001202513.2",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.608C>T",
"hgvs_p": "p.Thr203Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001189442.1",
"strand": true,
"transcript": "NM_001202513.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 220,
"aa_ref": "T",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5578,
"cdna_start": 862,
"cds_end": null,
"cds_length": 663,
"cds_start": 608,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000876182.1",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.608C>T",
"hgvs_p": "p.Thr203Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546241.1",
"strand": true,
"transcript": "ENST00000876182.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 220,
"aa_ref": "T",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3250,
"cdna_start": 830,
"cds_end": null,
"cds_length": 663,
"cds_start": 608,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000876183.1",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.608C>T",
"hgvs_p": "p.Thr203Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546242.1",
"strand": true,
"transcript": "ENST00000876183.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 211,
"aa_ref": "T",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5519,
"cdna_start": 803,
"cds_end": null,
"cds_length": 636,
"cds_start": 581,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001202514.2",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.581C>T",
"hgvs_p": "p.Thr194Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001189443.1",
"strand": true,
"transcript": "NM_001202514.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 180,
"aa_ref": "T",
"aa_start": 172,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 860,
"cdna_start": 830,
"cds_end": null,
"cds_length": 545,
"cds_start": 515,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000435990.5",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "c.515C>T",
"hgvs_p": "p.Thr172Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000410672.1",
"strand": true,
"transcript": "ENST00000435990.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 490,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000465446.1",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "n.78C>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": "ENST00000465446.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1577,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_170375.1",
"gene_hgnc_id": 26321,
"gene_symbol": "ASPRV1",
"hgvs_c": "n.1101-5036G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_170375.1",
"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": 982,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000409442.2",
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"hgvs_c": "n.*479C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000386523.2",
"strand": true,
"transcript": "ENST00000409442.2",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs144479868",
"effect": "missense_variant",
"frequency_reference_population": 0.00022737749,
"gene_hgnc_id": 6761,
"gene_symbol": "MXD1",
"gnomad_exomes_ac": 343,
"gnomad_exomes_af": 0.000234628,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 24,
"gnomad_genomes_af": 0.000157722,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.854,
"pos": 69938229,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.146,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002357.4"
}
]
}