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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: 19-49864191-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49864191&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49864191,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_007254.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "NM_007254.4",
"protein_id": "NP_009185.2",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 521,
"cds_start": 624,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000322344.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007254.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000322344.8",
"protein_id": "ENSP00000323511.2",
"transcript_support_level": 1,
"aa_start": 208,
"aa_end": null,
"aa_length": 521,
"cds_start": 624,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007254.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322344.8"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000596014.5",
"protein_id": "ENSP00000472300.1",
"transcript_support_level": 1,
"aa_start": 208,
"aa_end": null,
"aa_length": 521,
"cds_start": 624,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596014.5"
},
{
"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": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*551C>T",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"transcript_support_level": 1,
"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": "ENST00000593946.5"
},
{
"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": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*551C>T",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"transcript_support_level": 1,
"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": "ENST00000593946.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.651C>T",
"hgvs_p": "p.Ala217Ala",
"transcript": "ENST00000861313.1",
"protein_id": "ENSP00000531372.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 530,
"cds_start": 651,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861313.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.651C>T",
"hgvs_p": "p.Ala217Ala",
"transcript": "ENST00000934451.1",
"protein_id": "ENSP00000604510.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 530,
"cds_start": 651,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934451.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934445.1",
"protein_id": "ENSP00000604504.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 521,
"cds_start": 624,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934445.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934450.1",
"protein_id": "ENSP00000604509.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 521,
"cds_start": 624,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934450.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934449.1",
"protein_id": "ENSP00000604508.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 514,
"cds_start": 624,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934449.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.591C>T",
"hgvs_p": "p.Ala197Ala",
"transcript": "ENST00000965095.1",
"protein_id": "ENSP00000635154.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 510,
"cds_start": 591,
"cds_end": null,
"cds_length": 1533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965095.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934448.1",
"protein_id": "ENSP00000604507.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 508,
"cds_start": 624,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934448.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000861311.1",
"protein_id": "ENSP00000531370.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 507,
"cds_start": 624,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861311.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000600573.5",
"protein_id": "ENSP00000469826.1",
"transcript_support_level": 5,
"aa_start": 208,
"aa_end": null,
"aa_length": 490,
"cds_start": 624,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600573.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000631020.2",
"protein_id": "ENSP00000486707.1",
"transcript_support_level": 5,
"aa_start": 208,
"aa_end": null,
"aa_length": 485,
"cds_start": 624,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000631020.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.498C>T",
"hgvs_p": "p.Ala166Ala",
"transcript": "ENST00000861312.1",
"protein_id": "ENSP00000531371.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 479,
"cds_start": 498,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861312.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.498C>T",
"hgvs_p": "p.Ala166Ala",
"transcript": "ENST00000965096.1",
"protein_id": "ENSP00000635155.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 479,
"cds_start": 498,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965096.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.477C>T",
"hgvs_p": "p.Ala159Ala",
"transcript": "ENST00000965094.1",
"protein_id": "ENSP00000635153.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 472,
"cds_start": 477,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965094.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934444.1",
"protein_id": "ENSP00000604503.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 471,
"cds_start": 624,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934444.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000600910.5",
"protein_id": "ENSP00000473137.1",
"transcript_support_level": 5,
"aa_start": 208,
"aa_end": null,
"aa_length": 455,
"cds_start": 624,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600910.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.624C>T",
"hgvs_p": "p.Ala208Ala",
"transcript": "ENST00000934447.1",
"protein_id": "ENSP00000604506.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 455,
"cds_start": 624,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934447.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.393C>T",
"hgvs_p": "p.Ala131Ala",
"transcript": "ENST00000934446.1",
"protein_id": "ENSP00000604505.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 444,
"cds_start": 393,
"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": "ENST00000934446.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
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"bayesdelnoaf_score": -0.8,
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"acmg_by_gene": [
{
"score": -14,
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"pathogenic_score": 0,
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"BP6",
"BP7",
"BS1",
"BS2"
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"verdict": "Benign",
"transcript": "NM_007254.4",
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],
"clinvar_disease": " 12,Developmental and epileptic encephalopathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"phenotype_combined": "not specified|not provided|Developmental and epileptic encephalopathy, 12",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}