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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-123403094-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=123403094&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 123403094,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000620443.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln",
"transcript": "NM_000828.5",
"protein_id": "NP_000819.4",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 894,
"cds_start": 1181,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": null,
"mane_plus": "ENST00000622768.5",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln",
"transcript": "NM_007325.5",
"protein_id": "NP_015564.5",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 894,
"cds_start": 1181,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": "ENST00000620443.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln",
"transcript": "ENST00000620443.2",
"protein_id": "ENSP00000478489.1",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 894,
"cds_start": 1181,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": "NM_007325.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln",
"transcript": "ENST00000622768.5",
"protein_id": "ENSP00000481554.1",
"transcript_support_level": 5,
"aa_start": 394,
"aa_end": null,
"aa_length": 894,
"cds_start": 1181,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": null,
"mane_plus": "NM_000828.5",
"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": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"hgvs_c": "n.1181G>A",
"hgvs_p": null,
"transcript": "ENST00000620581.4",
"protein_id": "ENSP00000481875.1",
"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": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.412+34156C>T",
"hgvs_p": null,
"transcript": "ENST00000825206.1",
"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": 1629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.601+42925C>T",
"hgvs_p": null,
"transcript": "ENST00000825207.1",
"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": 1185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.406+42925C>T",
"hgvs_p": null,
"transcript": "ENST00000825208.1",
"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": 717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.463-33516C>T",
"hgvs_p": null,
"transcript": "ENST00000825209.1",
"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": 941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.348-33516C>T",
"hgvs_p": null,
"transcript": "ENST00000825210.1",
"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": 829,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.408-33516C>T",
"hgvs_p": null,
"transcript": "ENST00000825211.1",
"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": 668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.707-21873C>T",
"hgvs_p": null,
"transcript": "ENST00000825212.1",
"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": 1431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.583-4300C>T",
"hgvs_p": null,
"transcript": "ENST00000825213.1",
"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": 795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307341",
"gene_hgnc_id": null,
"hgvs_c": "n.407-4300C>T",
"hgvs_p": null,
"transcript": "ENST00000825214.1",
"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": 617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GRIA3",
"gene_hgnc_id": 4573,
"dbsnp": "rs138817389",
"frequency_reference_population": 0.0010222632,
"hom_count_reference_population": 369,
"allele_count_reference_population": 1060,
"gnomad_exomes_af": 0.00103704,
"gnomad_genomes_af": 0.000900435,
"gnomad_exomes_ac": 959,
"gnomad_genomes_ac": 101,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010767817497253418,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.335,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0852,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"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": -15,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 16,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000620443.2",
"gene_symbol": "GRIA3",
"hgnc_id": 4573,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000825206.1",
"gene_symbol": "ENSG00000307341",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.412+34156C>T",
"hgvs_p": null
}
],
"clinvar_disease": "GRIA3-related disorder,Inborn genetic diseases,Syndromic X-linked intellectual disability 94,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:4",
"phenotype_combined": "not specified|not provided|Syndromic X-linked intellectual disability 94|GRIA3-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}