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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: 8-3219437-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=3219437&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 3219437,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_033225.6",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4490A>G",
"hgvs_p": "p.Asn1497Ser",
"transcript": "NM_033225.6",
"protein_id": "NP_150094.5",
"transcript_support_level": null,
"aa_start": 1497,
"aa_end": null,
"aa_length": 3564,
"cds_start": 4490,
"cds_end": null,
"cds_length": 10695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000635120.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033225.6"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4490A>G",
"hgvs_p": "p.Asn1497Ser",
"transcript": "ENST00000635120.2",
"protein_id": "ENSP00000489225.1",
"transcript_support_level": 5,
"aa_start": 1497,
"aa_end": null,
"aa_length": 3564,
"cds_start": 4490,
"cds_end": null,
"cds_length": 10695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033225.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635120.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.2930A>G",
"hgvs_p": "p.Asn977Ser",
"transcript": "ENST00000335551.11",
"protein_id": "ENSP00000334828.6",
"transcript_support_level": 1,
"aa_start": 977,
"aa_end": null,
"aa_length": 2966,
"cds_start": 2930,
"cds_end": null,
"cds_length": 8901,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335551.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "n.2023A>G",
"hgvs_p": null,
"transcript": "ENST00000523488.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000523488.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4493A>G",
"hgvs_p": "p.Asn1498Ser",
"transcript": "ENST00000520002.5",
"protein_id": "ENSP00000430733.1",
"transcript_support_level": 5,
"aa_start": 1498,
"aa_end": null,
"aa_length": 3565,
"cds_start": 4493,
"cds_end": null,
"cds_length": 10698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000520002.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4493A>G",
"hgvs_p": "p.Asn1498Ser",
"transcript": "ENST00000602557.5",
"protein_id": "ENSP00000473359.1",
"transcript_support_level": 5,
"aa_start": 1498,
"aa_end": null,
"aa_length": 3565,
"cds_start": 4493,
"cds_end": null,
"cds_length": 10698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602557.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4493A>G",
"hgvs_p": "p.Asn1498Ser",
"transcript": "ENST00000400186.7",
"protein_id": "ENSP00000383047.3",
"transcript_support_level": 5,
"aa_start": 1498,
"aa_end": null,
"aa_length": 3388,
"cds_start": 4493,
"cds_end": null,
"cds_length": 10167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000400186.7"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4493A>G",
"hgvs_p": "p.Asn1498Ser",
"transcript": "ENST00000602723.5",
"protein_id": "ENSP00000473617.1",
"transcript_support_level": 5,
"aa_start": 1498,
"aa_end": null,
"aa_length": 3388,
"cds_start": 4493,
"cds_end": null,
"cds_length": 10167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602723.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4490A>G",
"hgvs_p": "p.Asn1497Ser",
"transcript": "XM_011534752.3",
"protein_id": "XP_011533054.1",
"transcript_support_level": null,
"aa_start": 1497,
"aa_end": null,
"aa_length": 3549,
"cds_start": 4490,
"cds_end": null,
"cds_length": 10650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534752.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.4490A>G",
"hgvs_p": "p.Asn1497Ser",
"transcript": "XM_017013731.2",
"protein_id": "XP_016869220.1",
"transcript_support_level": null,
"aa_start": 1497,
"aa_end": null,
"aa_length": 3327,
"cds_start": 4490,
"cds_end": null,
"cds_length": 9984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017013731.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.1583A>G",
"hgvs_p": "p.Asn528Ser",
"transcript": "XM_011534753.4",
"protein_id": "XP_011533055.1",
"transcript_support_level": null,
"aa_start": 528,
"aa_end": null,
"aa_length": 2595,
"cds_start": 1583,
"cds_end": null,
"cds_length": 7788,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534753.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "c.512A>G",
"hgvs_p": "p.Asn171Ser",
"transcript": "XM_011534754.2",
"protein_id": "XP_011533056.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 2238,
"cds_start": 512,
"cds_end": null,
"cds_length": 6717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534754.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"hgvs_c": "n.723A>G",
"hgvs_p": null,
"transcript": "ENST00000523387.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000523387.5"
}
],
"gene_symbol": "CSMD1",
"gene_hgnc_id": 14026,
"dbsnp": "rs28455997",
"frequency_reference_population": 0.12845768,
"hom_count_reference_population": 13111,
"allele_count_reference_population": 190215,
"gnomad_exomes_af": 0.130866,
"gnomad_genomes_af": 0.107435,
"gnomad_exomes_ac": 173863,
"gnomad_genomes_ac": 16352,
"gnomad_exomes_homalt": 11939,
"gnomad_genomes_homalt": 1172,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0017918050289154053,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20000000298023224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.131,
"revel_prediction": "Benign",
"alphamissense_score": 0.0677,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.136,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.2,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_033225.6",
"gene_symbol": "CSMD1",
"hgnc_id": 14026,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4490A>G",
"hgvs_p": "p.Asn1497Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}