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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-68432906-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=68432906&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 68432906,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000355520.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "NM_002547.3",
"protein_id": "NP_002538.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 802,
"cds_start": 115,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 7569,
"mane_select": "ENST00000355520.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000355520.6",
"protein_id": "ENSP00000347710.5",
"transcript_support_level": 1,
"aa_start": 39,
"aa_end": null,
"aa_length": 802,
"cds_start": 115,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 7569,
"mane_select": "NM_002547.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000681408.1",
"protein_id": "ENSP00000506619.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 767,
"cds_start": 115,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 820,
"cdna_end": null,
"cdna_length": 3783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "NM_001437258.1",
"protein_id": "NP_001424187.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 694,
"cds_start": 115,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 7245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000679748.1",
"protein_id": "ENSP00000505800.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 694,
"cds_start": 115,
"cds_end": null,
"cds_length": 2085,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 3314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000679822.1",
"protein_id": "ENSP00000505810.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 641,
"cds_start": 115,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 115,
"cdna_end": null,
"cdna_length": 5534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000680612.1",
"protein_id": "ENSP00000505365.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 597,
"cds_start": 115,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 332,
"cdna_end": null,
"cdna_length": 2140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000491714.2",
"protein_id": "ENSP00000506478.1",
"transcript_support_level": 3,
"aa_start": 39,
"aa_end": null,
"aa_length": 68,
"cds_start": 115,
"cds_end": null,
"cds_length": 207,
"cdna_start": 402,
"cdna_end": null,
"cdna_length": 598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "ENST00000680804.1",
"protein_id": "ENSP00000505428.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 68,
"cds_start": 115,
"cds_end": null,
"cds_length": 207,
"cdna_start": 253,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "XM_011530961.2",
"protein_id": "XP_011529263.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 802,
"cds_start": 115,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 7452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "XM_006724653.3",
"protein_id": "XP_006724716.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 793,
"cds_start": 115,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 7527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "XM_017029555.2",
"protein_id": "XP_016885044.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 565,
"cds_start": 115,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 8125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile",
"transcript": "XM_047442145.1",
"protein_id": "XP_047298101.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 565,
"cds_start": 115,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 330,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.474G>A",
"hgvs_p": null,
"transcript": "ENST00000679914.1",
"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": 3296,
"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": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.432G>A",
"hgvs_p": null,
"transcript": "ENST00000680262.1",
"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": 964,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.792G>A",
"hgvs_p": null,
"transcript": "ENST00000680503.1",
"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": 5372,
"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": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.759G>A",
"hgvs_p": null,
"transcript": "ENST00000680595.1",
"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": 1599,
"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": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.247G>A",
"hgvs_p": null,
"transcript": "ENST00000681349.1",
"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": 1247,
"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": "OPHN1",
"gene_hgnc_id": 8148,
"hgvs_c": "n.163G>A",
"hgvs_p": null,
"transcript": "ENST00000681520.1",
"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": 621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPHN1",
"gene_hgnc_id": 8148,
"dbsnp": "rs41303733",
"frequency_reference_population": 0.07409968,
"hom_count_reference_population": 31333,
"allele_count_reference_population": 89689,
"gnomad_exomes_af": 0.0757855,
"gnomad_genomes_af": 0.0576599,
"gnomad_exomes_ac": 83198,
"gnomad_genomes_ac": 6491,
"gnomad_exomes_homalt": 2375,
"gnomad_genomes_homalt": 180,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0017223358154296875,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.104,
"revel_prediction": "Benign",
"alphamissense_score": 0.2433,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.148,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000355520.6",
"gene_symbol": "OPHN1",
"hgnc_id": 8148,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.115G>A",
"hgvs_p": "p.Val39Ile"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}