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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: X-153862698-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153862698&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153862698,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000425.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3739A>G",
"hgvs_p": "p.Thr1247Ala",
"transcript": "NM_001278116.2",
"protein_id": "NP_001265045.1",
"transcript_support_level": null,
"aa_start": 1247,
"aa_end": null,
"aa_length": 1257,
"cds_start": 3739,
"cds_end": null,
"cds_length": 3774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370060.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278116.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3739A>G",
"hgvs_p": "p.Thr1247Ala",
"transcript": "ENST00000370060.7",
"protein_id": "ENSP00000359077.1",
"transcript_support_level": 5,
"aa_start": 1247,
"aa_end": null,
"aa_length": 1257,
"cds_start": 3739,
"cds_end": null,
"cds_length": 3774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001278116.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370060.7"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3727A>G",
"hgvs_p": "p.Thr1243Ala",
"transcript": "ENST00000361699.8",
"protein_id": "ENSP00000355380.4",
"transcript_support_level": 1,
"aa_start": 1243,
"aa_end": null,
"aa_length": 1253,
"cds_start": 3727,
"cds_end": null,
"cds_length": 3762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361699.8"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3712A>G",
"hgvs_p": "p.Thr1238Ala",
"transcript": "ENST00000361981.7",
"protein_id": "ENSP00000354712.3",
"transcript_support_level": 1,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1248,
"cds_start": 3712,
"cds_end": null,
"cds_length": 3747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361981.7"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3781A>G",
"hgvs_p": "p.Thr1261Ala",
"transcript": "ENST00000891165.1",
"protein_id": "ENSP00000561224.1",
"transcript_support_level": null,
"aa_start": 1261,
"aa_end": null,
"aa_length": 1271,
"cds_start": 3781,
"cds_end": null,
"cds_length": 3816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891165.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3739A>G",
"hgvs_p": "p.Thr1247Ala",
"transcript": "NM_000425.5",
"protein_id": "NP_000416.1",
"transcript_support_level": null,
"aa_start": 1247,
"aa_end": null,
"aa_length": 1257,
"cds_start": 3739,
"cds_end": null,
"cds_length": 3774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000425.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3727A>G",
"hgvs_p": "p.Thr1243Ala",
"transcript": "NM_024003.3",
"protein_id": "NP_076493.1",
"transcript_support_level": null,
"aa_start": 1243,
"aa_end": null,
"aa_length": 1253,
"cds_start": 3727,
"cds_end": null,
"cds_length": 3762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024003.3"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3712A>G",
"hgvs_p": "p.Thr1238Ala",
"transcript": "NM_001143963.2",
"protein_id": "NP_001137435.1",
"transcript_support_level": null,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1248,
"cds_start": 3712,
"cds_end": null,
"cds_length": 3747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001143963.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3712A>G",
"hgvs_p": "p.Thr1238Ala",
"transcript": "ENST00000370055.5",
"protein_id": "ENSP00000359072.1",
"transcript_support_level": 5,
"aa_start": 1238,
"aa_end": null,
"aa_length": 1248,
"cds_start": 3712,
"cds_end": null,
"cds_length": 3747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370055.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3709A>G",
"hgvs_p": "p.Thr1237Ala",
"transcript": "ENST00000891164.1",
"protein_id": "ENSP00000561223.1",
"transcript_support_level": null,
"aa_start": 1237,
"aa_end": null,
"aa_length": 1247,
"cds_start": 3709,
"cds_end": null,
"cds_length": 3744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891164.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3577A>G",
"hgvs_p": "p.Thr1193Ala",
"transcript": "ENST00000912312.1",
"protein_id": "ENSP00000582371.1",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1203,
"cds_start": 3577,
"cds_end": null,
"cds_length": 3612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912312.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.3568A>G",
"hgvs_p": "p.Thr1190Ala",
"transcript": "ENST00000912311.1",
"protein_id": "ENSP00000582370.1",
"transcript_support_level": null,
"aa_start": 1190,
"aa_end": null,
"aa_length": 1200,
"cds_start": 3568,
"cds_end": null,
"cds_length": 3603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912311.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.427A>G",
"hgvs_p": "p.Thr143Ala",
"transcript": "ENST00000370058.7",
"protein_id": "ENSP00000359075.3",
"transcript_support_level": 3,
"aa_start": 143,
"aa_end": null,
"aa_length": 153,
"cds_start": 427,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370058.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "n.*94A>G",
"hgvs_p": null,
"transcript": "ENST00000491983.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000491983.1"
}
],
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"dbsnp": "rs781854219",
"frequency_reference_population": 0.0000049572927,
"hom_count_reference_population": 1,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000455575,
"gnomad_genomes_af": 0.00000886336,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06974539160728455,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.0735,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.887,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_000425.5",
"gene_symbol": "L1CAM",
"hgnc_id": 6470,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3739A>G",
"hgvs_p": "p.Thr1247Ala"
}
],
"clinvar_disease": "Spastic paraplegia",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Spastic paraplegia",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}