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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: 3-196248245-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196248245&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196248245,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000431016.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "NM_001312673.2",
"protein_id": "NP_001299602.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 367,
"cds_start": 296,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 5546,
"mane_select": "ENST00000431016.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000431016.6",
"protein_id": "ENSP00000394617.1",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 367,
"cds_start": 296,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 5546,
"mane_select": "NM_001312673.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000292823.6",
"protein_id": "ENSP00000292823.2",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 367,
"cds_start": 296,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 469,
"cdna_end": null,
"cdna_length": 5597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272741",
"gene_hgnc_id": null,
"hgvs_c": "n.*302C>T",
"hgvs_p": null,
"transcript": "ENST00000431391.1",
"protein_id": "ENSP00000405181.1",
"transcript_support_level": 5,
"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": 708,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.444C>T",
"hgvs_p": null,
"transcript": "ENST00000460677.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1393,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.449C>T",
"hgvs_p": null,
"transcript": "ENST00000473978.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272741",
"gene_hgnc_id": null,
"hgvs_c": "n.*302C>T",
"hgvs_p": null,
"transcript": "ENST00000431391.1",
"protein_id": "ENSP00000405181.1",
"transcript_support_level": 5,
"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": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000419333.5",
"protein_id": "ENSP00000390968.1",
"transcript_support_level": 5,
"aa_start": 99,
"aa_end": null,
"aa_length": 380,
"cds_start": 296,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 306,
"cdna_end": null,
"cdna_length": 1325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "NM_005017.4",
"protein_id": "NP_005008.2",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 367,
"cds_start": 296,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 482,
"cdna_end": null,
"cdna_length": 5610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"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": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000411591.5",
"protein_id": "ENSP00000400430.1",
"transcript_support_level": 3,
"aa_start": 99,
"aa_end": null,
"aa_length": 292,
"cds_start": 296,
"cds_end": null,
"cds_length": 879,
"cdna_start": 501,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000441879.5",
"protein_id": "ENSP00000392397.1",
"transcript_support_level": 3,
"aa_start": 99,
"aa_end": null,
"aa_length": 211,
"cds_start": 296,
"cds_end": null,
"cds_length": 638,
"cdna_start": 382,
"cdna_end": null,
"cdna_length": 724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.98C>T",
"hgvs_p": "p.Ala33Val",
"transcript": "ENST00000430755.5",
"protein_id": "ENSP00000402283.1",
"transcript_support_level": 3,
"aa_start": 33,
"aa_end": null,
"aa_length": 201,
"cds_start": 98,
"cds_end": null,
"cds_length": 606,
"cdna_start": 98,
"cdna_end": null,
"cdna_length": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000412869.5",
"protein_id": "ENSP00000402015.1",
"transcript_support_level": 3,
"aa_start": 99,
"aa_end": null,
"aa_length": 132,
"cds_start": 296,
"cds_end": null,
"cds_length": 401,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val",
"transcript": "ENST00000443555.1",
"protein_id": "ENSP00000393341.1",
"transcript_support_level": 5,
"aa_start": 99,
"aa_end": null,
"aa_length": 114,
"cds_start": 296,
"cds_end": null,
"cds_length": 345,
"cdna_start": 500,
"cdna_end": null,
"cdna_length": 549,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.*109C>T",
"hgvs_p": null,
"transcript": "ENST00000438634.5",
"protein_id": "ENSP00000391405.1",
"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": 555,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.296C>T",
"hgvs_p": null,
"transcript": "ENST00000444822.5",
"protein_id": "ENSP00000397888.1",
"transcript_support_level": 3,
"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": 724,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.29C>T",
"hgvs_p": null,
"transcript": "ENST00000488235.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 466,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.355C>T",
"hgvs_p": null,
"transcript": "ENST00000491544.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.*109C>T",
"hgvs_p": null,
"transcript": "ENST00000438634.5",
"protein_id": "ENSP00000391405.1",
"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": 555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"dbsnp": "rs587777189",
"frequency_reference_population": 0.000013025647,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000116433,
"gnomad_genomes_af": 0.0000262923,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9561529755592346,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.976,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9428,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.599,
"phylop100way_prediction": "Pathogenic",
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000431016.6",
"gene_symbol": "PCYT1A",
"hgnc_id": 8754,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.296C>T",
"hgvs_p": "p.Ala99Val"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000431391.1",
"gene_symbol": "ENSG00000272741",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*302C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}