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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: 3-196226965-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196226965&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196226965,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_152672.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp",
"transcript": "NM_152672.6",
"protein_id": "NP_689885.4",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 340,
"cds_start": 134,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296327.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152672.6"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp",
"transcript": "ENST00000296327.10",
"protein_id": "ENSP00000296327.5",
"transcript_support_level": 1,
"aa_start": 45,
"aa_end": null,
"aa_length": 340,
"cds_start": 134,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152672.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296327.10"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp",
"transcript": "ENST00000900647.1",
"protein_id": "ENSP00000570706.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 340,
"cds_start": 134,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900647.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp",
"transcript": "ENST00000900649.1",
"protein_id": "ENSP00000570708.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 337,
"cds_start": 134,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900649.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp",
"transcript": "ENST00000900648.1",
"protein_id": "ENSP00000570707.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 314,
"cds_start": 134,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900648.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.44C>A",
"hgvs_p": "p.Ala15Asp",
"transcript": "ENST00000428985.1",
"protein_id": "ENSP00000413951.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 210,
"cds_start": 44,
"cds_end": null,
"cds_length": 634,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428985.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.-215C>A",
"hgvs_p": null,
"transcript": "XM_047447662.1",
"protein_id": "XP_047303618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447662.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.-215C>A",
"hgvs_p": null,
"transcript": "XM_047447662.1",
"protein_id": "XP_047303618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447662.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.487-12592G>T",
"hgvs_p": null,
"transcript": "ENST00000441879.5",
"protein_id": "ENSP00000392397.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441879.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "n.*146C>A",
"hgvs_p": null,
"transcript": "ENST00000442203.1",
"protein_id": "ENSP00000391172.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000442203.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "n.312C>A",
"hgvs_p": null,
"transcript": "ENST00000472653.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000472653.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "n.47C>A",
"hgvs_p": null,
"transcript": "ENST00000476129.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000476129.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "n.*146C>A",
"hgvs_p": null,
"transcript": "ENST00000442203.1",
"protein_id": "ENSP00000391172.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000442203.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000309772",
"gene_hgnc_id": null,
"hgvs_c": "n.228+1172G>T",
"hgvs_p": null,
"transcript": "ENST00000843822.1",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000843822.1"
}
],
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"dbsnp": "rs770488941",
"frequency_reference_population": 0.0000037221444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000342497,
"gnomad_genomes_af": 0.00000657436,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15372169017791748,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.033,
"revel_prediction": "Benign",
"alphamissense_score": 0.1048,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.38,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000141089136521215,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_152672.6",
"gene_symbol": "SLC51A",
"hgnc_id": 29955,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.134C>A",
"hgvs_p": "p.Ala45Asp"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000441879.5",
"gene_symbol": "PCYT1A",
"hgnc_id": 8754,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.487-12592G>T",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000843822.1",
"gene_symbol": "ENSG00000309772",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.228+1172G>T",
"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
}