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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-153868424-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153868424&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153868424,
"ref": "T",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_000425.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr",
"transcript": "NM_001278116.2",
"protein_id": "NP_001265045.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1257,
"cds_start": 1581,
"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": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr",
"transcript": "ENST00000370060.7",
"protein_id": "ENSP00000359077.1",
"transcript_support_level": 5,
"aa_start": 527,
"aa_end": null,
"aa_length": 1257,
"cds_start": 1581,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr",
"transcript": "ENST00000361699.8",
"protein_id": "ENSP00000355380.4",
"transcript_support_level": 1,
"aa_start": 527,
"aa_end": null,
"aa_length": 1253,
"cds_start": 1581,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "ENST00000361981.7",
"protein_id": "ENSP00000354712.3",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 1248,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "ENST00000891165.1",
"protein_id": "ENSP00000561224.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 1271,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr",
"transcript": "NM_000425.5",
"protein_id": "NP_000416.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1257,
"cds_start": 1581,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr",
"transcript": "NM_024003.3",
"protein_id": "NP_076493.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 1253,
"cds_start": 1581,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "NM_001143963.2",
"protein_id": "NP_001137435.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 1248,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "ENST00000370055.5",
"protein_id": "ENSP00000359072.1",
"transcript_support_level": 5,
"aa_start": 522,
"aa_end": null,
"aa_length": 1248,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "ENST00000891164.1",
"protein_id": "ENSP00000561223.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 1247,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1566A>C",
"hgvs_p": "p.Thr522Thr",
"transcript": "ENST00000912312.1",
"protein_id": "ENSP00000582371.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 1203,
"cds_start": 1566,
"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": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "c.1422A>C",
"hgvs_p": "p.Thr474Thr",
"transcript": "ENST00000912311.1",
"protein_id": "ENSP00000582370.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 1200,
"cds_start": 1422,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.534A>C",
"hgvs_p": null,
"transcript": "ENST00000484652.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000484652.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"hgvs_c": "n.200A>C",
"hgvs_p": null,
"transcript": "ENST00000496122.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000496122.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_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.-49A>C",
"hgvs_p": null,
"transcript": "ENST00000455590.1",
"protein_id": "ENSP00000397792.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": null,
"cds_end": null,
"cds_length": 568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000455590.1"
}
],
"gene_symbol": "L1CAM",
"gene_hgnc_id": 6470,
"dbsnp": "rs201131192",
"frequency_reference_population": 0.0003222536,
"hom_count_reference_population": 212,
"allele_count_reference_population": 390,
"gnomad_exomes_af": 0.000340549,
"gnomad_genomes_af": 0.000142857,
"gnomad_exomes_ac": 374,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 2,
"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": -1.597,
"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": "NM_000425.5",
"gene_symbol": "L1CAM",
"hgnc_id": 6470,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1581A>C",
"hgvs_p": "p.Thr527Thr"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Inborn genetic diseases,Spastic paraplegia,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "not specified|Spastic paraplegia|Hereditary spastic paraplegia|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}