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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-153865707-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153865707&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "L1CAM",
"hgnc_id": 6470,
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"inheritance_mode": "XL",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000425.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.55,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Spastic paraplegia,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.550000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1257,
"aa_ref": "Y",
"aa_start": 848,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5138,
"cdna_start": 2761,
"cds_end": null,
"cds_length": 3774,
"cds_start": 2544,
"consequences": [
"stop_gained"
],
"exon_count": 29,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001278116.2",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370060.7",
"protein_coding": true,
"protein_id": "NP_001265045.1",
"strand": false,
"transcript": "NM_001278116.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1257,
"aa_ref": "Y",
"aa_start": 848,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5138,
"cdna_start": 2761,
"cds_end": null,
"cds_length": 3774,
"cds_start": 2544,
"consequences": [
"stop_gained"
],
"exon_count": 29,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000370060.7",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001278116.2",
"protein_coding": true,
"protein_id": "ENSP00000359077.1",
"strand": false,
"transcript": "ENST00000370060.7",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1253,
"aa_ref": "Y",
"aa_start": 848,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3888,
"cdna_start": 2555,
"cds_end": null,
"cds_length": 3762,
"cds_start": 2544,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000361699.8",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355380.4",
"strand": false,
"transcript": "ENST00000361699.8",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1248,
"aa_ref": "Y",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5004,
"cdna_start": 2637,
"cds_end": null,
"cds_length": 3747,
"cds_start": 2529,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000361981.7",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2529C>A",
"hgvs_p": "p.Tyr843*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000354712.3",
"strand": false,
"transcript": "ENST00000361981.7",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1271,
"aa_ref": "Y",
"aa_start": 866,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4993,
"cdna_start": 2783,
"cds_end": null,
"cds_length": 3816,
"cds_start": 2598,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000891165.1",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2598C>A",
"hgvs_p": "p.Tyr866*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561224.1",
"strand": false,
"transcript": "ENST00000891165.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1257,
"aa_ref": "Y",
"aa_start": 848,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5099,
"cdna_start": 2722,
"cds_end": null,
"cds_length": 3774,
"cds_start": 2544,
"consequences": [
"stop_gained"
],
"exon_count": 28,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_000425.5",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_000416.1",
"strand": false,
"transcript": "NM_000425.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1253,
"aa_ref": "Y",
"aa_start": 848,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5019,
"cdna_start": 2652,
"cds_end": null,
"cds_length": 3762,
"cds_start": 2544,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_024003.3",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2544C>A",
"hgvs_p": "p.Tyr848*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_076493.1",
"strand": false,
"transcript": "NM_024003.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1248,
"aa_ref": "Y",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5004,
"cdna_start": 2637,
"cds_end": null,
"cds_length": 3747,
"cds_start": 2529,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_001143963.2",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2529C>A",
"hgvs_p": "p.Tyr843*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001137435.1",
"strand": false,
"transcript": "NM_001143963.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1248,
"aa_ref": "Y",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4655,
"cdna_start": 2727,
"cds_end": null,
"cds_length": 3747,
"cds_start": 2529,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000370055.5",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2529C>A",
"hgvs_p": "p.Tyr843*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000359072.1",
"strand": false,
"transcript": "ENST00000370055.5",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1247,
"aa_ref": "Y",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5111,
"cdna_start": 2744,
"cds_end": null,
"cds_length": 3744,
"cds_start": 2529,
"consequences": [
"stop_gained"
],
"exon_count": 27,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000891164.1",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2529C>A",
"hgvs_p": "p.Tyr843*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561223.1",
"strand": false,
"transcript": "ENST00000891164.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1203,
"aa_ref": "Y",
"aa_start": 843,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4979,
"cdna_start": 2749,
"cds_end": null,
"cds_length": 3612,
"cds_start": 2529,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000912312.1",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2529C>A",
"hgvs_p": "p.Tyr843*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582371.1",
"strand": false,
"transcript": "ENST00000912312.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1200,
"aa_ref": "Y",
"aa_start": 795,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4998,
"cdna_start": 2633,
"cds_end": null,
"cds_length": 3603,
"cds_start": 2385,
"consequences": [
"stop_gained"
],
"exon_count": 26,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000912311.1",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "c.2385C>A",
"hgvs_p": "p.Tyr795*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582370.1",
"strand": false,
"transcript": "ENST00000912311.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000474853.1",
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"hgvs_c": "n.209C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000474853.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs886039410",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 6470,
"gene_symbol": "L1CAM",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "not provided|Spastic paraplegia",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.57,
"pos": 153865707,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000425.5"
}
]
}