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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-68197209-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=68197209&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 68197209,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000355520.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "NM_002547.3",
"protein_id": "NP_002538.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 802,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 7569,
"mane_select": "ENST00000355520.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "ENST00000355520.6",
"protein_id": "ENSP00000347710.5",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 802,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 7569,
"mane_select": "NM_002547.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.976G>C",
"hgvs_p": "p.Glu326Gln",
"transcript": "ENST00000681408.1",
"protein_id": "ENSP00000506619.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 767,
"cds_start": 976,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 1681,
"cdna_end": null,
"cdna_length": 3783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "NM_001437258.1",
"protein_id": "NP_001424187.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 694,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 7245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "ENST00000679748.1",
"protein_id": "ENSP00000505800.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 694,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 3314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "ENST00000679822.1",
"protein_id": "ENSP00000505810.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 641,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 5534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "ENST00000680612.1",
"protein_id": "ENSP00000505365.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 597,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1298,
"cdna_end": null,
"cdna_length": 2140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.364G>C",
"hgvs_p": "p.Glu122Gln",
"transcript": "ENST00000467444.1",
"protein_id": "ENSP00000505570.1",
"transcript_support_level": 5,
"aa_start": 122,
"aa_end": null,
"aa_length": 226,
"cds_start": 364,
"cds_end": null,
"cds_length": 681,
"cdna_start": 365,
"cdna_end": null,
"cdna_length": 737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "XM_011530961.2",
"protein_id": "XP_011529263.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 802,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 1296,
"cdna_end": null,
"cdna_length": 7452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "XM_006724653.3",
"protein_id": "XP_006724716.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 793,
"cds_start": 1081,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 7527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.778G>C",
"hgvs_p": "p.Glu260Gln",
"transcript": "XM_047442144.1",
"protein_id": "XP_047298100.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 701,
"cds_start": 778,
"cds_end": null,
"cds_length": 2106,
"cdna_start": 1379,
"cdna_end": null,
"cdna_length": 7535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "XM_017029555.2",
"protein_id": "XP_016885044.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 565,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 8125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln",
"transcript": "XM_047442145.1",
"protein_id": "XP_047298101.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 565,
"cds_start": 1081,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1296,
"cdna_end": null,
"cdna_length": 8008,
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.587G>C",
"hgvs_p": null,
"transcript": "ENST00000680592.1",
"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": 2138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"dbsnp": "rs1555952056",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6710042953491211,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.252,
"revel_prediction": "Benign",
"alphamissense_score": 0.623,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.948,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000355520.6",
"gene_symbol": "OPHN1",
"hgnc_id": 8148,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1081G>C",
"hgvs_p": "p.Glu361Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}