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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-153872156-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153872156&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153872156,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000370060.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "NM_001278116.2",
"protein_id": "NP_001265045.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 1257,
"cds_start": 396,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 5138,
"mane_select": "ENST00000370060.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "ENST00000370060.7",
"protein_id": "ENSP00000359077.1",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 1257,
"cds_start": 396,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 5138,
"mane_select": "NM_001278116.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "ENST00000361699.8",
"protein_id": "ENSP00000355380.4",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 1253,
"cds_start": 396,
"cds_end": null,
"cds_length": 3762,
"cdna_start": 407,
"cdna_end": null,
"cdna_length": 3888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.381C>T",
"hgvs_p": "p.Ala127Ala",
"transcript": "ENST00000361981.7",
"protein_id": "ENSP00000354712.3",
"transcript_support_level": 1,
"aa_start": 127,
"aa_end": null,
"aa_length": 1248,
"cds_start": 381,
"cds_end": null,
"cds_length": 3747,
"cdna_start": 489,
"cdna_end": null,
"cdna_length": 5004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "NM_000425.5",
"protein_id": "NP_000416.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 1257,
"cds_start": 396,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 574,
"cdna_end": null,
"cdna_length": 5099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "NM_024003.3",
"protein_id": "NP_076493.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 1253,
"cds_start": 396,
"cds_end": null,
"cds_length": 3762,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 5019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.381C>T",
"hgvs_p": "p.Ala127Ala",
"transcript": "NM_001143963.2",
"protein_id": "NP_001137435.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 1248,
"cds_start": 381,
"cds_end": null,
"cds_length": 3747,
"cdna_start": 489,
"cdna_end": null,
"cdna_length": 5004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.381C>T",
"hgvs_p": "p.Ala127Ala",
"transcript": "ENST00000370055.5",
"protein_id": "ENSP00000359072.1",
"transcript_support_level": 5,
"aa_start": 127,
"aa_end": null,
"aa_length": 1248,
"cds_start": 381,
"cds_end": null,
"cds_length": 3747,
"cdna_start": 579,
"cdna_end": null,
"cdna_length": 4655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala",
"transcript": "ENST00000439496.5",
"protein_id": "ENSP00000402407.1",
"transcript_support_level": 4,
"aa_start": 132,
"aa_end": null,
"aa_length": 149,
"cds_start": 396,
"cds_end": null,
"cds_length": 452,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.381C>T",
"hgvs_p": "p.Ala127Ala",
"transcript": "ENST00000407935.6",
"protein_id": "ENSP00000384902.2",
"transcript_support_level": 3,
"aa_start": 127,
"aa_end": null,
"aa_length": 127,
"cds_start": 381,
"cds_end": null,
"cds_length": 385,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.*438C>T",
"hgvs_p": null,
"transcript": "ENST00000646191.1",
"protein_id": "ENSP00000493873.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.*111C>T",
"hgvs_p": null,
"transcript": "ENST00000420165.5",
"protein_id": "ENSP00000392524.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 89,
"cds_start": -4,
"cds_end": null,
"cds_length": 270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.*145C>T",
"hgvs_p": null,
"transcript": "ENST00000458029.1",
"protein_id": "ENSP00000396079.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 82,
"cds_start": -4,
"cds_end": null,
"cds_length": 251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.*65C>T",
"hgvs_p": null,
"transcript": "ENST00000464967.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.*302C>T",
"hgvs_p": null,
"transcript": "ENST00000642393.1",
"protein_id": "ENSP00000495119.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"dbsnp": "rs144708625",
"frequency_reference_population": 0.00041957916,
"hom_count_reference_population": 122,
"allele_count_reference_population": 505,
"gnomad_exomes_af": 0.000340082,
"gnomad_genomes_af": 0.00121203,
"gnomad_exomes_ac": 372,
"gnomad_genomes_ac": 133,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.823,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000370060.7",
"gene_symbol": "L1CAM",
"hgnc_id": 6470,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Ala132Ala"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000646191.1",
"gene_symbol": "ENSG00000284987",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*438C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Spastic paraplegia,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:3",
"phenotype_combined": "not specified|not provided|Spastic paraplegia|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}