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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: 22-24321550-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=24321550&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 24321550,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000314328.14",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "NM_015330.6",
"protein_id": "NP_056145.5",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 1117,
"cds_start": 570,
"cds_end": null,
"cds_length": 3354,
"cdna_start": 864,
"cdna_end": null,
"cdna_length": 6763,
"mane_select": "ENST00000314328.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "ENST00000314328.14",
"protein_id": "ENSP00000325785.8",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 1117,
"cds_start": 570,
"cds_end": null,
"cds_length": 3354,
"cdna_start": 864,
"cdna_end": null,
"cdna_length": 6763,
"mane_select": "NM_015330.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "ENST00000437398.5",
"protein_id": "ENSP00000393363.1",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 1117,
"cds_start": 570,
"cds_end": null,
"cds_length": 3354,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 6674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L-ADORA2A",
"gene_hgnc_id": 49185,
"hgvs_c": "n.570G>A",
"hgvs_p": null,
"transcript": "ENST00000358654.2",
"protein_id": "ENSP00000351480.2",
"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": 6204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.627G>A",
"hgvs_p": "p.Thr209Thr",
"transcript": "ENST00000651059.1",
"protein_id": "ENSP00000499052.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 1136,
"cds_start": 627,
"cds_end": null,
"cds_length": 3411,
"cdna_start": 915,
"cdna_end": null,
"cdna_length": 6282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "NM_001145468.4",
"protein_id": "NP_001138940.4",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 1117,
"cds_start": 570,
"cds_end": null,
"cds_length": 3354,
"cdna_start": 760,
"cdna_end": null,
"cdna_length": 6659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "NM_001254732.3",
"protein_id": "NP_001241661.3",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 1078,
"cds_start": 570,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 760,
"cdna_end": null,
"cdna_length": 6542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "ENST00000541492.1",
"protein_id": "ENSP00000439633.1",
"transcript_support_level": 2,
"aa_start": 190,
"aa_end": null,
"aa_length": 1078,
"cds_start": 570,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 708,
"cdna_end": null,
"cdna_length": 3525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr",
"transcript": "ENST00000421374.5",
"protein_id": "ENSP00000405671.1",
"transcript_support_level": 2,
"aa_start": 190,
"aa_end": null,
"aa_length": 787,
"cds_start": 570,
"cds_end": null,
"cds_length": 2366,
"cdna_start": 769,
"cdna_end": null,
"cdna_length": 2565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "c.387G>A",
"hgvs_p": "p.Thr129Thr",
"transcript": "ENST00000440893.1",
"protein_id": "ENSP00000414354.1",
"transcript_support_level": 3,
"aa_start": 129,
"aa_end": null,
"aa_length": 174,
"cds_start": 387,
"cds_end": null,
"cds_length": 525,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000299949",
"gene_hgnc_id": null,
"hgvs_c": "n.242C>T",
"hgvs_p": null,
"transcript": "ENST00000767633.1",
"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": 570,
"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": "ENSG00000299949",
"gene_hgnc_id": null,
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"transcript": "ENST00000767634.1",
"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": 685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000299949",
"gene_hgnc_id": null,
"hgvs_c": "n.304C>T",
"hgvs_p": null,
"transcript": "ENST00000767635.1",
"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": 630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPECC1L-ADORA2A",
"gene_hgnc_id": 49185,
"hgvs_c": "n.878G>A",
"hgvs_p": null,
"transcript": "NR_103546.1",
"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": 6289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"hgvs_c": "n.481+227G>A",
"hgvs_p": null,
"transcript": "ENST00000416735.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPECC1L",
"gene_hgnc_id": 29022,
"dbsnp": "rs3747113",
"frequency_reference_population": 0.25315407,
"hom_count_reference_population": 53073,
"allele_count_reference_population": 408576,
"gnomad_exomes_af": 0.256094,
"gnomad_genomes_af": 0.224909,
"gnomad_exomes_ac": 374357,
"gnomad_genomes_ac": 34219,
"gnomad_exomes_homalt": 48919,
"gnomad_genomes_homalt": 4154,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.416,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000314328.14",
"gene_symbol": "SPECC1L",
"hgnc_id": 29022,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.570G>A",
"hgvs_p": "p.Thr190Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000358654.2",
"gene_symbol": "SPECC1L-ADORA2A",
"hgnc_id": 49185,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.570G>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000767633.1",
"gene_symbol": "ENSG00000299949",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.242C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant Opitz G/BBB syndrome,Oculomaxillofacial dysostosis,Teebi hypertelorism syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not provided|Autosomal dominant Opitz G/BBB syndrome|Teebi hypertelorism syndrome|Oculomaxillofacial dysostosis|not specified",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}