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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: 1-33527223-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=33527223&ref=G&alt=A&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": "CSMD2",
"hgnc_id": 19290,
"hgvs_c": "c.10207C>T",
"hgvs_p": "p.Arg3403Trp",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001281956.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 1548,
"alphamissense_prediction": null,
"alphamissense_score": 0.1203,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "1",
"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": 0.07296165823936462,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3631,
"aa_ref": "R",
"aa_start": 3403,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13655,
"cdna_start": 10340,
"cds_end": null,
"cds_length": 10896,
"cds_start": 10207,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "NM_001281956.2",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10207C>T",
"hgvs_p": "p.Arg3403Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000373381.9",
"protein_coding": true,
"protein_id": "NP_001268885.1",
"strand": false,
"transcript": "NM_001281956.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3631,
"aa_ref": "R",
"aa_start": 3403,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13655,
"cdna_start": 10340,
"cds_end": null,
"cds_length": 10896,
"cds_start": 10207,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "ENST00000373381.9",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10207C>T",
"hgvs_p": "p.Arg3403Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001281956.2",
"protein_coding": true,
"protein_id": "ENSP00000362479.4",
"strand": false,
"transcript": "ENST00000373381.9",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3487,
"aa_ref": "R",
"aa_start": 3259,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13108,
"cdna_start": 9804,
"cds_end": null,
"cds_length": 10464,
"cds_start": 9775,
"consequences": [
"missense_variant"
],
"exon_count": 70,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "ENST00000373388.7",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.9775C>T",
"hgvs_p": "p.Arg3259Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000362486.3",
"strand": false,
"transcript": "ENST00000373388.7",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3591,
"aa_ref": "R",
"aa_start": 3363,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13430,
"cdna_start": 10116,
"cds_end": null,
"cds_length": 10776,
"cds_start": 10087,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "ENST00000619121.4",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10087C>T",
"hgvs_p": "p.Arg3363Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000483463.1",
"strand": false,
"transcript": "ENST00000619121.4",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3487,
"aa_ref": "R",
"aa_start": 3259,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13119,
"cdna_start": 9804,
"cds_end": null,
"cds_length": 10464,
"cds_start": 9775,
"consequences": [
"missense_variant"
],
"exon_count": 70,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "NM_052896.5",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.9775C>T",
"hgvs_p": "p.Arg3259Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_443128.2",
"strand": false,
"transcript": "NM_052896.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3607,
"aa_ref": "R",
"aa_start": 3379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16477,
"cdna_start": 10268,
"cds_end": null,
"cds_length": 10824,
"cds_start": 10135,
"consequences": [
"missense_variant"
],
"exon_count": 70,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_017000185.2",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10135C>T",
"hgvs_p": "p.Arg3379Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016855674.1",
"strand": false,
"transcript": "XM_017000185.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3607,
"aa_ref": "R",
"aa_start": 3379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13583,
"cdna_start": 10268,
"cds_end": null,
"cds_length": 10824,
"cds_start": 10135,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_047443607.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10135C>T",
"hgvs_p": "p.Arg3379Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299563.1",
"strand": false,
"transcript": "XM_047443607.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3606,
"aa_ref": "R",
"aa_start": 3378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13580,
"cdna_start": 10265,
"cds_end": null,
"cds_length": 10821,
"cds_start": 10132,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_047443642.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10132C>T",
"hgvs_p": "p.Arg3378Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299598.1",
"strand": false,
"transcript": "XM_047443642.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3567,
"aa_ref": "R",
"aa_start": 3339,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13359,
"cdna_start": 10044,
"cds_end": null,
"cds_length": 10704,
"cds_start": 10015,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_047443656.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10015C>T",
"hgvs_p": "p.Arg3339Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299612.1",
"strand": false,
"transcript": "XM_047443656.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3566,
"aa_ref": "R",
"aa_start": 3338,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13356,
"cdna_start": 10041,
"cds_end": null,
"cds_length": 10701,
"cds_start": 10012,
"consequences": [
"missense_variant"
],
"exon_count": 71,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_047443685.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10012C>T",
"hgvs_p": "p.Arg3338Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299641.1",
"strand": false,
"transcript": "XM_047443685.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3506,
"aa_ref": "R",
"aa_start": 3379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10892,
"cdna_start": 10268,
"cds_end": null,
"cds_length": 10521,
"cds_start": 10135,
"consequences": [
"missense_variant"
],
"exon_count": 68,
"exon_rank": 65,
"exon_rank_end": null,
"feature": "XM_047443661.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.10135C>T",
"hgvs_p": "p.Arg3379Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299617.1",
"strand": false,
"transcript": "XM_047443661.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 3362,
"aa_ref": "R",
"aa_start": 3134,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12848,
"cdna_start": 9533,
"cds_end": null,
"cds_length": 10089,
"cds_start": 9400,
"consequences": [
"missense_variant"
],
"exon_count": 65,
"exon_rank": 59,
"exon_rank_end": null,
"feature": "XM_047443666.1",
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"hgvs_c": "c.9400C>T",
"hgvs_p": "p.Arg3134Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299622.1",
"strand": false,
"transcript": "XM_047443666.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149656829",
"effect": "missense_variant",
"frequency_reference_population": 0.0009591304,
"gene_hgnc_id": 19290,
"gene_symbol": "CSMD2",
"gnomad_exomes_ac": 1441,
"gnomad_exomes_af": 0.000985766,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 107,
"gnomad_genomes_af": 0.000703235,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.332,
"pos": 33527223,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.117,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05999999865889549,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.06,
"transcript": "NM_001281956.2"
}
]
}