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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: 2-1666323-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=1666323&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 1666323,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_012293.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1182T>C",
"hgvs_p": "p.Ser394Ser",
"transcript": "NM_012293.3",
"protein_id": "NP_036425.1",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 1479,
"cds_start": 1182,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 1242,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "ENST00000252804.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012293.3"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1182T>C",
"hgvs_p": "p.Ser394Ser",
"transcript": "ENST00000252804.9",
"protein_id": "ENSP00000252804.4",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 1479,
"cds_start": 1182,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 1242,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "NM_012293.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252804.9"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1167T>C",
"hgvs_p": "p.Ser389Ser",
"transcript": "ENST00000433670.5",
"protein_id": "ENSP00000402738.1",
"transcript_support_level": 1,
"aa_start": 389,
"aa_end": null,
"aa_length": 722,
"cds_start": 1167,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 2643,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433670.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1110T>C",
"hgvs_p": "p.Ser370Ser",
"transcript": "ENST00000857505.1",
"protein_id": "ENSP00000527564.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 1455,
"cds_start": 1110,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 1469,
"cdna_end": null,
"cdna_length": 7040,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857505.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1110T>C",
"hgvs_p": "p.Ser370Ser",
"transcript": "ENST00000425171.2",
"protein_id": "ENSP00000398363.2",
"transcript_support_level": 5,
"aa_start": 370,
"aa_end": null,
"aa_length": 691,
"cds_start": 1110,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1157,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425171.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.1110T>C",
"hgvs_p": "p.Ser370Ser",
"transcript": "XM_005264707.4",
"protein_id": "XP_005264764.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 1455,
"cds_start": 1110,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 1170,
"cdna_end": null,
"cdna_length": 6745,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264707.4"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.633T>C",
"hgvs_p": "p.Ser211Ser",
"transcript": "XM_011510396.2",
"protein_id": "XP_011508698.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 1296,
"cds_start": 633,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1080,
"cdna_end": null,
"cdna_length": 6655,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510396.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.633T>C",
"hgvs_p": "p.Ser211Ser",
"transcript": "XM_047445788.1",
"protein_id": "XP_047301744.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 1296,
"cds_start": 633,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1040,
"cdna_end": null,
"cdna_length": 6615,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445788.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.633T>C",
"hgvs_p": "p.Ser211Ser",
"transcript": "XM_047445789.1",
"protein_id": "XP_047301745.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 1296,
"cds_start": 633,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 6579,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445789.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.374T>C",
"hgvs_p": null,
"transcript": "ENST00000467191.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 567,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000467191.5"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.580T>C",
"hgvs_p": null,
"transcript": "ENST00000478155.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000478155.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.528T>C",
"hgvs_p": null,
"transcript": "ENST00000483018.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 593,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000483018.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.*33T>C",
"hgvs_p": null,
"transcript": "ENST00000477810.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 543,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000477810.1"
}
],
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"dbsnp": "rs76057922",
"frequency_reference_population": 0.0025884907,
"hom_count_reference_population": 88,
"allele_count_reference_population": 4178,
"gnomad_exomes_af": 0.0015003,
"gnomad_genomes_af": 0.0130287,
"gnomad_exomes_ac": 2193,
"gnomad_genomes_ac": 1985,
"gnomad_exomes_homalt": 36,
"gnomad_genomes_homalt": 52,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01600000075995922,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.016,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.853,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_012293.3",
"gene_symbol": "PXDN",
"hgnc_id": 14966,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1182T>C",
"hgvs_p": "p.Ser394Ser"
}
],
"clinvar_disease": "Anterior segment dysgenesis 7,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Anterior segment dysgenesis 7|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}