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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: 3-74285487-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=74285487&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 74285487,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020872.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2522G>A",
"hgvs_p": "p.Arg841Gln",
"transcript": "NM_020872.3",
"protein_id": "NP_065923.1",
"transcript_support_level": null,
"aa_start": 841,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2522,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263665.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020872.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2522G>A",
"hgvs_p": "p.Arg841Gln",
"transcript": "ENST00000263665.7",
"protein_id": "ENSP00000263665.6",
"transcript_support_level": 1,
"aa_start": 841,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2522,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020872.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263665.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2522G>A",
"hgvs_p": "p.Arg841Gln",
"transcript": "NM_001393376.1",
"protein_id": "NP_001380305.1",
"transcript_support_level": null,
"aa_start": 841,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2522,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393376.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2516G>A",
"hgvs_p": "p.Arg839Gln",
"transcript": "ENST00000962150.1",
"protein_id": "ENSP00000632209.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2516,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962150.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2207G>A",
"hgvs_p": "p.Arg736Gln",
"transcript": "ENST00000962149.1",
"protein_id": "ENSP00000632208.1",
"transcript_support_level": null,
"aa_start": 736,
"aa_end": null,
"aa_length": 923,
"cds_start": 2207,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962149.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2030G>A",
"hgvs_p": "p.Arg677Gln",
"transcript": "ENST00000906976.1",
"protein_id": "ENSP00000577035.1",
"transcript_support_level": null,
"aa_start": 677,
"aa_end": null,
"aa_length": 864,
"cds_start": 2030,
"cds_end": null,
"cds_length": 2595,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906976.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2522G>A",
"hgvs_p": "p.Arg841Gln",
"transcript": "XM_011533768.3",
"protein_id": "XP_011532070.1",
"transcript_support_level": null,
"aa_start": 841,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2522,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533768.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.2348G>A",
"hgvs_p": "p.Arg783Gln",
"transcript": "XM_017006508.2",
"protein_id": "XP_016861997.1",
"transcript_support_level": null,
"aa_start": 783,
"aa_end": null,
"aa_length": 970,
"cds_start": 2348,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006508.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"hgvs_c": "c.1196G>A",
"hgvs_p": "p.Arg399Gln",
"transcript": "XM_017006509.1",
"protein_id": "XP_016861998.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 586,
"cds_start": 1196,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006509.1"
}
],
"gene_symbol": "CNTN3",
"gene_hgnc_id": 2173,
"dbsnp": "rs199931035",
"frequency_reference_population": 0.000343182,
"hom_count_reference_population": 0,
"allele_count_reference_population": 552,
"gnomad_exomes_af": 0.000336397,
"gnomad_genomes_af": 0.000408265,
"gnomad_exomes_ac": 490,
"gnomad_genomes_ac": 62,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009720057249069214,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.116,
"revel_prediction": "Benign",
"alphamissense_score": 0.1631,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.632,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_020872.3",
"gene_symbol": "CNTN3",
"hgnc_id": 2173,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2522G>A",
"hgvs_p": "p.Arg841Gln"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}