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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: 11-65868015-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=65868015&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 65868015,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000307998.11",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.1016A>T",
"hgvs_p": "p.Gln339Leu",
"transcript": "NM_016938.5",
"protein_id": "NP_058634.4",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 443,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1141,
"cdna_end": null,
"cdna_length": 1934,
"mane_select": "ENST00000307998.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.1016A>T",
"hgvs_p": "p.Gln339Leu",
"transcript": "ENST00000307998.11",
"protein_id": "ENSP00000309953.6",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 443,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1141,
"cdna_end": null,
"cdna_length": 1934,
"mane_select": "NM_016938.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.1016A>T",
"hgvs_p": null,
"transcript": "ENST00000531972.5",
"protein_id": "ENSP00000435295.1",
"transcript_support_level": 1,
"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": 1813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.1016A>T",
"hgvs_p": "p.Gln339Leu",
"transcript": "ENST00000528176.5",
"protein_id": "ENSP00000434151.1",
"transcript_support_level": 5,
"aa_start": 339,
"aa_end": null,
"aa_length": 436,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1311,
"cdna_start": 1084,
"cdna_end": null,
"cdna_length": 1504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.164A>T",
"hgvs_p": "p.Gln55Leu",
"transcript": "ENST00000531645.5",
"protein_id": "ENSP00000436521.1",
"transcript_support_level": 3,
"aa_start": 55,
"aa_end": null,
"aa_length": 182,
"cds_start": 164,
"cds_end": null,
"cds_length": 549,
"cdna_start": 164,
"cdna_end": null,
"cdna_length": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.177A>T",
"hgvs_p": null,
"transcript": "ENST00000525392.1",
"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": 519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.1582A>T",
"hgvs_p": null,
"transcript": "ENST00000526628.5",
"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": 2277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.249A>T",
"hgvs_p": null,
"transcript": "ENST00000528409.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.2010A>T",
"hgvs_p": null,
"transcript": "ENST00000531005.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 2135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.442A>T",
"hgvs_p": null,
"transcript": "ENST00000532084.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.1141A>T",
"hgvs_p": null,
"transcript": "NR_037718.2",
"protein_id": null,
"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": 1802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.-24-2A>T",
"hgvs_p": null,
"transcript": "ENST00000530806.5",
"protein_id": "ENSP00000436526.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 75,
"cds_start": -4,
"cds_end": null,
"cds_length": 230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "c.-8A>T",
"hgvs_p": null,
"transcript": "ENST00000526911.1",
"protein_id": "ENSP00000436536.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 74,
"cds_start": -4,
"cds_end": null,
"cds_length": 225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"hgvs_c": "n.-110A>T",
"hgvs_p": null,
"transcript": "ENST00000524408.1",
"protein_id": "ENSP00000432191.1",
"transcript_support_level": 5,
"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": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EFEMP2",
"gene_hgnc_id": 3219,
"dbsnp": "rs754118526",
"frequency_reference_population": 0.000008674596,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000752546,
"gnomad_genomes_af": 0.0000197104,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14328539371490479,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.245,
"revel_prediction": "Benign",
"alphamissense_score": 0.1428,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.083,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.1,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000307998.11",
"gene_symbol": "EFEMP2",
"hgnc_id": 3219,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1016A>T",
"hgvs_p": "p.Gln339Leu"
}
],
"clinvar_disease": " autosomal recessive, type 1B,Cutis laxa,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Cutis laxa, autosomal recessive, type 1B|not provided|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}