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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: 3-101801427-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=101801427&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 101801427,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_145037.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_145037.4",
"protein_id": "NP_659474.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000273347.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145037.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000273347.10",
"protein_id": "ENSP00000273347.5",
"transcript_support_level": 1,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_145037.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000273347.10"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000477909.5",
"protein_id": "ENSP00000418369.1",
"transcript_support_level": 1,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000477909.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001134456.2",
"protein_id": "NP_001127928.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134456.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348990.2",
"protein_id": "NP_001335919.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348990.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348991.2",
"protein_id": "NP_001335920.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348991.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348992.2",
"protein_id": "NP_001335921.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348992.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348993.2",
"protein_id": "NP_001335922.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348993.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348994.2",
"protein_id": "NP_001335923.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348994.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "NM_001348995.2",
"protein_id": "NP_001335924.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348995.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000474165.6",
"protein_id": "ENSP00000419667.2",
"transcript_support_level": 5,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474165.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000487830.2",
"protein_id": "ENSP00000515931.1",
"transcript_support_level": 3,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000487830.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000491511.6",
"protein_id": "ENSP00000417485.1",
"transcript_support_level": 2,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000491511.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000495842.6",
"protein_id": "ENSP00000418381.2",
"transcript_support_level": 5,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000495842.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000704530.1",
"protein_id": "ENSP00000515919.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704530.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000704532.1",
"protein_id": "ENSP00000515920.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704532.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000704539.1",
"protein_id": "ENSP00000515927.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704539.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000704551.1",
"protein_id": "ENSP00000515939.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704551.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000704552.1",
"protein_id": "ENSP00000515940.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000704552.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000879315.1",
"protein_id": "ENSP00000549374.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879315.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000925277.1",
"protein_id": "ENSP00000595336.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925277.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NXPE3",
"gene_hgnc_id": 28238,
"hgvs_c": "c.286C>T",
"hgvs_p": "p.Pro96Ser",
"transcript": "ENST00000925279.1",
"protein_id": "ENSP00000595338.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 559,
"cds_start": 286,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925279.1"
},
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],
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"computational_score_selected": 0.05828538537025452,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
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"phylop100way_prediction": "Benign",
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"spliceai_max_prediction": "Benign",
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"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
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"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_145037.4",
"gene_symbol": "NXPE3",
"hgnc_id": 28238,
"effects": [
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],
"inheritance_mode": "AR",
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],
"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
}