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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: 3-196248246-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196248246&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PCYT1A",
"hgnc_id": 8754,
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_005017.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000272741",
"hgnc_id": null,
"hgvs_c": "n.*301G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000431391.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Moderate",
"acmg_score": 8,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.9696,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.54,
"chr": "3",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9675680994987488,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5546,
"cdna_start": 417,
"cds_end": null,
"cds_length": 1104,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001312673.2",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000431016.6",
"protein_coding": true,
"protein_id": "NP_001299602.1",
"strand": false,
"transcript": "NM_001312673.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5546,
"cdna_start": 417,
"cds_end": null,
"cds_length": 1104,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000431016.6",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001312673.2",
"protein_coding": true,
"protein_id": "ENSP00000394617.1",
"strand": false,
"transcript": "ENST00000431016.6",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5597,
"cdna_start": 468,
"cds_end": null,
"cds_length": 1104,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000292823.6",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000292823.2",
"strand": false,
"transcript": "ENST00000292823.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000431391.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000272741",
"hgvs_c": "n.*301G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000405181.1",
"strand": false,
"transcript": "ENST00000431391.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1393,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000460677.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "n.443G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000460677.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1430,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000473978.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "n.448G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000473978.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000431391.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000272741",
"hgvs_c": "n.*301G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000405181.1",
"strand": false,
"transcript": "ENST00000431391.1",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 380,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1325,
"cdna_start": 305,
"cds_end": null,
"cds_length": 1143,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000419333.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000390968.1",
"strand": false,
"transcript": "ENST00000419333.5",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5610,
"cdna_start": 481,
"cds_end": null,
"cds_length": 1104,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_005017.4",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_005008.2",
"strand": false,
"transcript": "NM_005017.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 367,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3166,
"cdna_start": 590,
"cds_end": null,
"cds_length": 1104,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000875586.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545645.1",
"strand": false,
"transcript": "ENST00000875586.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 366,
"aa_ref": "A",
"aa_start": 98,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2126,
"cdna_start": 362,
"cds_end": null,
"cds_length": 1101,
"cds_start": 292,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000875587.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.292G>A",
"hgvs_p": "p.Ala98Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545646.1",
"strand": false,
"transcript": "ENST00000875587.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 356,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5522,
"cdna_start": 426,
"cds_end": null,
"cds_length": 1071,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000875583.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545642.1",
"strand": false,
"transcript": "ENST00000875583.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 356,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2146,
"cdna_start": 418,
"cds_end": null,
"cds_length": 1071,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000928611.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000598670.1",
"strand": false,
"transcript": "ENST00000928611.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 304,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3120,
"cdna_start": 458,
"cds_end": null,
"cds_length": 915,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000875584.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545643.1",
"strand": false,
"transcript": "ENST00000875584.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 293,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3069,
"cdna_start": 410,
"cds_end": null,
"cds_length": 882,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000875585.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000545644.1",
"strand": false,
"transcript": "ENST00000875585.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 292,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1084,
"cdna_start": 500,
"cds_end": null,
"cds_length": 879,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000411591.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000400430.1",
"strand": false,
"transcript": "ENST00000411591.5",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 211,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 724,
"cdna_start": 381,
"cds_end": null,
"cds_length": 638,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000441879.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392397.1",
"strand": false,
"transcript": "ENST00000441879.5",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 201,
"aa_ref": "A",
"aa_start": 33,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 798,
"cdna_start": 97,
"cds_end": null,
"cds_length": 606,
"cds_start": 97,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000430755.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.97G>A",
"hgvs_p": "p.Ala33Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402283.1",
"strand": false,
"transcript": "ENST00000430755.5",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 132,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 499,
"cdna_start": 393,
"cds_end": null,
"cds_length": 401,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000412869.5",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402015.1",
"strand": false,
"transcript": "ENST00000412869.5",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 114,
"aa_ref": "A",
"aa_start": 99,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 549,
"cdna_start": 499,
"cds_end": null,
"cds_length": 345,
"cds_start": 295,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000443555.1",
"gene_hgnc_id": 8754,
"gene_symbol": "PCYT1A",
"hgvs_c": "c.295G>A",
"hgvs_p": "p.Ala99Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393341.1",
"strand": false,
"transcript": "ENST00000443555.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
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]
}