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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: 13-110512039-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=110512039&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"PP3",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL4A2",
"hgnc_id": 2203,
"hgvs_c": "c.4987G>A",
"hgvs_p": "p.Gly1663Ser",
"inheritance_mode": "AD",
"pathogenic_score": 1,
"score": -7,
"transcript": "NM_001846.4",
"verdict": "Benign"
},
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000289010",
"hgnc_id": null,
"hgvs_c": "n.150+8711C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 1,
"score": -3,
"transcript": "ENST00000793035.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BS1,BS2",
"acmg_score": -7,
"allele_count_reference_population": 1161,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.6241,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"chr": "13",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Inborn genetic diseases,Optic nerve hypoplasia,Porencephaly 2,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2 LB:3 B:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8149747848510742,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1712,
"aa_ref": "G",
"aa_start": 1663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6446,
"cdna_start": 5276,
"cds_end": null,
"cds_length": 5139,
"cds_start": 4987,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "NM_001846.4",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4987G>A",
"hgvs_p": "p.Gly1663Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000360467.7",
"protein_coding": true,
"protein_id": "NP_001837.2",
"strand": true,
"transcript": "NM_001846.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1712,
"aa_ref": "G",
"aa_start": 1663,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6446,
"cdna_start": 5276,
"cds_end": null,
"cds_length": 5139,
"cds_start": 4987,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000360467.7",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4987G>A",
"hgvs_p": "p.Gly1663Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001846.4",
"protein_coding": true,
"protein_id": "ENSP00000353654.5",
"strand": true,
"transcript": "ENST00000360467.7",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1739,
"aa_ref": "G",
"aa_start": 1690,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6345,
"cdna_start": 5357,
"cds_end": null,
"cds_length": 5220,
"cds_start": 5068,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000714399.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.5068G>A",
"hgvs_p": "p.Gly1690Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519666.1",
"strand": true,
"transcript": "ENST00000714399.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1712,
"aa_ref": "G",
"aa_start": 1663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6333,
"cdna_start": 5163,
"cds_end": null,
"cds_length": 5139,
"cds_start": 4987,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000400163.8",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4987G>A",
"hgvs_p": "p.Gly1663Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000383027.4",
"strand": true,
"transcript": "ENST00000400163.8",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1712,
"aa_ref": "G",
"aa_start": 1663,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6221,
"cdna_start": 5233,
"cds_end": null,
"cds_length": 5139,
"cds_start": 4987,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000907576.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4987G>A",
"hgvs_p": "p.Gly1663Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577635.1",
"strand": true,
"transcript": "ENST00000907576.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1707,
"aa_ref": "G",
"aa_start": 1658,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6092,
"cdna_start": 5104,
"cds_end": null,
"cds_length": 5124,
"cds_start": 4972,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000907577.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4972G>A",
"hgvs_p": "p.Gly1658Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577636.1",
"strand": true,
"transcript": "ENST00000907577.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1699,
"aa_ref": "G",
"aa_start": 1650,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6254,
"cdna_start": 5268,
"cds_end": null,
"cds_length": 5100,
"cds_start": 4948,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000907571.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4948G>A",
"hgvs_p": "p.Gly1650Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577630.1",
"strand": true,
"transcript": "ENST00000907571.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1663,
"aa_ref": "G",
"aa_start": 1614,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6119,
"cdna_start": 5131,
"cds_end": null,
"cds_length": 4992,
"cds_start": 4840,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000907575.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4840G>A",
"hgvs_p": "p.Gly1614Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577634.1",
"strand": true,
"transcript": "ENST00000907575.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1644,
"aa_ref": "G",
"aa_start": 1595,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6077,
"cdna_start": 5089,
"cds_end": null,
"cds_length": 4935,
"cds_start": 4783,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000907573.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4783G>A",
"hgvs_p": "p.Gly1595Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577632.1",
"strand": true,
"transcript": "ENST00000907573.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1638,
"aa_ref": "G",
"aa_start": 1589,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6050,
"cdna_start": 5062,
"cds_end": null,
"cds_length": 4917,
"cds_start": 4765,
"consequences": [
"missense_variant"
],
"exon_count": 47,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000714396.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4765G>A",
"hgvs_p": "p.Gly1589Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519663.1",
"strand": true,
"transcript": "ENST00000714396.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1613,
"aa_ref": "G",
"aa_start": 1564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5969,
"cdna_start": 4981,
"cds_end": null,
"cds_length": 4842,
"cds_start": 4690,
"consequences": [
"missense_variant"
],
"exon_count": 46,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000907574.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4690G>A",
"hgvs_p": "p.Gly1564Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577633.1",
"strand": true,
"transcript": "ENST00000907574.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1403,
"aa_ref": "G",
"aa_start": 1354,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5362,
"cdna_start": 4374,
"cds_end": null,
"cds_length": 4212,
"cds_start": 4060,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000907572.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "c.4060G>A",
"hgvs_p": "p.Gly1354Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000577631.1",
"strand": true,
"transcript": "ENST00000907572.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 679,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000463084.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.585G>A",
"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": "ENST00000463084.1",
"transcript_support_level": 3
},
{
"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": 1663,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000648222.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.675G>A",
"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": "ENST00000648222.1",
"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": 3630,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000650225.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.2642G>A",
"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": "ENST00000650225.1",
"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": 6363,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000714397.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.*1723G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519664.1",
"strand": true,
"transcript": "ENST00000714397.1",
"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": 6547,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000714398.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.*2708G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519665.1",
"strand": true,
"transcript": "ENST00000714398.1",
"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": 6363,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000714397.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.*1723G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519664.1",
"strand": true,
"transcript": "ENST00000714397.1",
"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": 6547,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 49,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000714398.1",
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"hgvs_c": "n.*2708G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519665.1",
"strand": true,
"transcript": "ENST00000714398.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 723,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000793035.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000289010",
"hgvs_c": "n.150+8711C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000793035.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs12877501",
"effect": "missense_variant",
"frequency_reference_population": 0.0007195511,
"gene_hgnc_id": 2203,
"gene_symbol": "COL4A2",
"gnomad_exomes_ac": 1100,
"gnomad_exomes_af": 0.000752799,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 61,
"gnomad_genomes_af": 0.000400546,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 3,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Porencephaly 2|not provided|Optic nerve hypoplasia|Inborn genetic diseases|not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.537,
"pos": 110512039,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.903,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001846.4"
}
]
}