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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-38160997-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=38160997&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 38160997,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006307.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "NM_006307.5",
"protein_id": "NP_006298.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 464,
"cds_start": 711,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378533.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006307.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000378533.4",
"protein_id": "ENSP00000367794.3",
"transcript_support_level": 1,
"aa_start": 237,
"aa_end": null,
"aa_length": 464,
"cds_start": 711,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006307.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378533.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250349",
"gene_hgnc_id": null,
"hgvs_c": "c.172-505124G>C",
"hgvs_p": null,
"transcript": "ENST00000465127.1",
"protein_id": "ENSP00000417050.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 279,
"cds_start": null,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000465127.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000898757.1",
"protein_id": "ENSP00000568816.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 488,
"cds_start": 711,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898757.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000969691.1",
"protein_id": "ENSP00000639750.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 461,
"cds_start": 711,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969691.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.651C>G",
"hgvs_p": "p.Ile217Met",
"transcript": "NM_001170750.2",
"protein_id": "NP_001164221.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 444,
"cds_start": 651,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001170750.2"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.651C>G",
"hgvs_p": "p.Ile217Met",
"transcript": "ENST00000544439.5",
"protein_id": "ENSP00000440758.1",
"transcript_support_level": 2,
"aa_start": 217,
"aa_end": null,
"aa_length": 444,
"cds_start": 651,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544439.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.612C>G",
"hgvs_p": "p.Ile204Met",
"transcript": "ENST00000969694.1",
"protein_id": "ENSP00000639753.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 431,
"cds_start": 612,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969694.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.534C>G",
"hgvs_p": "p.Ile178Met",
"transcript": "NM_001170751.2",
"protein_id": "NP_001164222.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 405,
"cds_start": 534,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001170751.2"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.534C>G",
"hgvs_p": "p.Ile178Met",
"transcript": "ENST00000432886.6",
"protein_id": "ENSP00000411165.2",
"transcript_support_level": 2,
"aa_start": 178,
"aa_end": null,
"aa_length": 405,
"cds_start": 534,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000432886.6"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000969693.1",
"protein_id": "ENSP00000639752.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 404,
"cds_start": 711,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969693.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.474C>G",
"hgvs_p": "p.Ile158Met",
"transcript": "ENST00000969692.1",
"protein_id": "ENSP00000639751.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 385,
"cds_start": 474,
"cds_end": null,
"cds_length": 1158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969692.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.459C>G",
"hgvs_p": "p.Ile153Met",
"transcript": "ENST00000969690.1",
"protein_id": "ENSP00000639749.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 380,
"cds_start": 459,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969690.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "NM_001170752.2",
"protein_id": "NP_001164223.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 379,
"cds_start": 711,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001170752.2"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "ENST00000538295.5",
"protein_id": "ENSP00000445034.1",
"transcript_support_level": 2,
"aa_start": 237,
"aa_end": null,
"aa_length": 379,
"cds_start": 711,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538295.5"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.282C>G",
"hgvs_p": "p.Ile94Met",
"transcript": "ENST00000898758.1",
"protein_id": "ENSP00000568817.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 321,
"cds_start": 282,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898758.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met",
"transcript": "XM_017029893.3",
"protein_id": "XP_016885382.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 419,
"cds_start": 711,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029893.3"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.651C>G",
"hgvs_p": "p.Ile217Met",
"transcript": "XM_047442563.1",
"protein_id": "XP_047298519.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 399,
"cds_start": 651,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442563.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"hgvs_c": "c.651C>G",
"hgvs_p": "p.Ile217Met",
"transcript": "XM_047442564.1",
"protein_id": "XP_047298520.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 359,
"cds_start": 651,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442564.1"
}
],
"gene_symbol": "SRPX",
"gene_hgnc_id": 11309,
"dbsnp": "rs374069621",
"frequency_reference_population": 0.00008852237,
"hom_count_reference_population": 43,
"allele_count_reference_population": 107,
"gnomad_exomes_af": 0.000094767,
"gnomad_genomes_af": 0.0000269527,
"gnomad_exomes_ac": 104,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24905866384506226,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.154,
"revel_prediction": "Benign",
"alphamissense_score": 0.2351,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.333,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006307.5",
"gene_symbol": "SRPX",
"hgnc_id": 11309,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.711C>G",
"hgvs_p": "p.Ile237Met"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000465127.1",
"gene_symbol": "ENSG00000250349",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.172-505124G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}