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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: 6-35779401-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=35779401&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CLPSL2",
"hgnc_id": 21250,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_207409.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 10,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1436,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.65,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.19008004665374756,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 100,
"aa_ref": "T",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 426,
"cdna_start": 275,
"cds_end": null,
"cds_length": 303,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_207409.4",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000403376.4",
"protein_coding": true,
"protein_id": "NP_997292.2",
"strand": true,
"transcript": "NM_207409.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 100,
"aa_ref": "T",
"aa_start": 85,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 426,
"cdna_start": 275,
"cds_end": null,
"cds_length": 303,
"cds_start": 254,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000403376.4",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_207409.4",
"protein_coding": true,
"protein_id": "ENSP00000385898.3",
"strand": true,
"transcript": "ENST00000403376.4",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 153,
"aa_ref": "D",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 488,
"cdna_start": 337,
"cds_end": null,
"cds_length": 462,
"cds_start": 333,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000360454.6",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Asp111Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000353639.2",
"strand": true,
"transcript": "ENST00000360454.6",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 59,
"aa_ref": "T",
"aa_start": 44,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 371,
"cdna_start": 215,
"cds_end": null,
"cds_length": 180,
"cds_start": 131,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000924056.1",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "c.131C>T",
"hgvs_p": "p.Thr44Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594115.1",
"strand": true,
"transcript": "ENST00000924056.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 153,
"aa_ref": "D",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 505,
"cdna_start": 354,
"cds_end": null,
"cds_length": 462,
"cds_start": 333,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001286550.2",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Asp111Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273479.1",
"strand": true,
"transcript": "NM_001286550.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 313,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000467122.1",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "n.162C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000467122.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 532,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000481904.5",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "n.381C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000481904.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 528,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_104467.2",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "n.377C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_104467.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 405,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_104469.2",
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"hgvs_c": "n.254C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_104469.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1767918442",
"effect": "missense_variant",
"frequency_reference_population": 0.000006978172,
"gene_hgnc_id": 21250,
"gene_symbol": "CLPSL2",
"gnomad_exomes_ac": 10,
"gnomad_exomes_af": 0.00000697817,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -3.068,
"pos": 35779401,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.304,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_207409.4"
}
]
}