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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: 2-100932919-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=100932919&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 100932919,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002518.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "NM_002518.4",
"protein_id": "NP_002509.2",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000335681.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002518.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000335681.10",
"protein_id": "ENSP00000338283.5",
"transcript_support_level": 1,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002518.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335681.10"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000906777.1",
"protein_id": "ENSP00000576836.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906777.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000906778.1",
"protein_id": "ENSP00000576837.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906778.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000960863.1",
"protein_id": "ENSP00000630922.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960863.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000960864.1",
"protein_id": "ENSP00000630923.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 794,
"cds_start": 191,
"cds_end": null,
"cds_length": 2385,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960864.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000933582.1",
"protein_id": "ENSP00000603641.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 786,
"cds_start": 191,
"cds_end": null,
"cds_length": 2361,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933582.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "ENST00000960862.1",
"protein_id": "ENSP00000630921.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 778,
"cds_start": 191,
"cds_end": null,
"cds_length": 2337,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960862.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.158C>T",
"hgvs_p": "p.Ala53Val",
"transcript": "ENST00000448812.5",
"protein_id": "ENSP00000388528.1",
"transcript_support_level": 5,
"aa_start": 53,
"aa_end": null,
"aa_length": 256,
"cds_start": 158,
"cds_end": null,
"cds_length": 773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448812.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"transcript": "ENST00000427413.5",
"protein_id": "ENSP00000397595.2",
"transcript_support_level": 3,
"aa_start": 129,
"aa_end": null,
"aa_length": 206,
"cds_start": 386,
"cds_end": null,
"cds_length": 623,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427413.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Ala50Val",
"transcript": "ENST00000451740.1",
"protein_id": "ENSP00000395265.1",
"transcript_support_level": 3,
"aa_start": 50,
"aa_end": null,
"aa_length": 106,
"cds_start": 149,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451740.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.281C>T",
"hgvs_p": "p.Ala94Val",
"transcript": "XM_047444503.1",
"protein_id": "XP_047300459.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 854,
"cds_start": 281,
"cds_end": null,
"cds_length": 2565,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444503.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.233C>T",
"hgvs_p": "p.Ala78Val",
"transcript": "XM_047444504.1",
"protein_id": "XP_047300460.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 838,
"cds_start": 233,
"cds_end": null,
"cds_length": 2517,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444504.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_005263953.3",
"protein_id": "XP_005264010.2",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005263953.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_047444505.1",
"protein_id": "XP_047300461.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444505.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_047444506.1",
"protein_id": "XP_047300462.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 824,
"cds_start": 191,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444506.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_011511242.3",
"protein_id": "XP_011509544.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 794,
"cds_start": 191,
"cds_end": null,
"cds_length": 2385,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511242.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_047444502.1",
"protein_id": "XP_047300458.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 794,
"cds_start": 191,
"cds_end": null,
"cds_length": 2385,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444502.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_017004214.2",
"protein_id": "XP_016859703.2",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 778,
"cds_start": 191,
"cds_end": null,
"cds_length": 2337,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004214.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_005263959.3",
"protein_id": "XP_005264016.2",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 770,
"cds_start": 191,
"cds_end": null,
"cds_length": 2313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005263959.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_047444510.1",
"protein_id": "XP_047300466.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 770,
"cds_start": 191,
"cds_end": null,
"cds_length": 2313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444510.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPAS2",
"gene_hgnc_id": 7895,
"hgvs_c": "c.191C>T",
"hgvs_p": "p.Ala64Val",
"transcript": "XM_047444511.1",
"protein_id": "XP_047300467.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 740,
"cds_start": 191,
"cds_end": null,
"cds_length": 2223,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444511.1"
},
{
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{
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{
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"biotype": "pseudogene",
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{
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],
"gene_symbol": "NPAS2",
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"dbsnp": "rs183671025",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000171165,
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"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1264457106590271,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1899999976158142,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.113,
"revel_prediction": "Benign",
"alphamissense_score": 0.1827,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.533,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.19,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
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"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002518.4",
"gene_symbol": "NPAS2",
"hgnc_id": 7895,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
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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
}