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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: 2-1666266-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=1666266&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 1666266,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000252804.9",
"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.1239T>C",
"hgvs_p": "p.Ser413Ser",
"transcript": "NM_012293.3",
"protein_id": "NP_036425.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 1479,
"cds_start": 1239,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 1299,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "ENST00000252804.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.1239T>C",
"hgvs_p": "p.Ser413Ser",
"transcript": "ENST00000252804.9",
"protein_id": "ENSP00000252804.4",
"transcript_support_level": 1,
"aa_start": 413,
"aa_end": null,
"aa_length": 1479,
"cds_start": 1239,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 1299,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "NM_012293.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.1224T>C",
"hgvs_p": "p.Ser408Ser",
"transcript": "ENST00000433670.5",
"protein_id": "ENSP00000402738.1",
"transcript_support_level": 1,
"aa_start": 408,
"aa_end": null,
"aa_length": 722,
"cds_start": 1224,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 2643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.1167T>C",
"hgvs_p": "p.Ser389Ser",
"transcript": "ENST00000425171.2",
"protein_id": "ENSP00000398363.2",
"transcript_support_level": 5,
"aa_start": 389,
"aa_end": null,
"aa_length": 691,
"cds_start": 1167,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1214,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.1167T>C",
"hgvs_p": "p.Ser389Ser",
"transcript": "XM_005264707.4",
"protein_id": "XP_005264764.1",
"transcript_support_level": null,
"aa_start": 389,
"aa_end": null,
"aa_length": 1455,
"cds_start": 1167,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 1227,
"cdna_end": null,
"cdna_length": 6745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.690T>C",
"hgvs_p": "p.Ser230Ser",
"transcript": "XM_011510396.2",
"protein_id": "XP_011508698.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 1296,
"cds_start": 690,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1137,
"cdna_end": null,
"cdna_length": 6655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.690T>C",
"hgvs_p": "p.Ser230Ser",
"transcript": "XM_047445788.1",
"protein_id": "XP_047301744.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 1296,
"cds_start": 690,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 6615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.690T>C",
"hgvs_p": "p.Ser230Ser",
"transcript": "XM_047445789.1",
"protein_id": "XP_047301745.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 1296,
"cds_start": 690,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 1061,
"cdna_end": null,
"cdna_length": 6579,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.431T>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 567,
"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": 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.637T>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3840,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.585T>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.*90T>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"dbsnp": "rs759183762",
"frequency_reference_population": 0.000007435276,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000684137,
"gnomad_genomes_af": 0.0000131378,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03200000151991844,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.032,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.251,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000252804.9",
"gene_symbol": "PXDN",
"hgnc_id": 14966,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1239T>C",
"hgvs_p": "p.Ser413Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}