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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: 3-45731317-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=45731317&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 45731317,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001319071.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "NM_014016.5",
"protein_id": "NP_054735.3",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 587,
"cds_start": 938,
"cds_end": null,
"cds_length": 1764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000389061.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014016.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000389061.10",
"protein_id": "ENSP00000373713.4",
"transcript_support_level": 1,
"aa_start": 313,
"aa_end": null,
"aa_length": 587,
"cds_start": 938,
"cds_end": null,
"cds_length": 1764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014016.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389061.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "n.629C>T",
"hgvs_p": null,
"transcript": "ENST00000455997.5",
"protein_id": "ENSP00000389975.1",
"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": "ENST00000455997.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "NM_001319071.2",
"protein_id": "NP_001306000.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 609,
"cds_start": 938,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319071.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000672858.2",
"protein_id": "ENSP00000500542.2",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 609,
"cds_start": 938,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000672858.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000972135.1",
"protein_id": "ENSP00000642194.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 604,
"cds_start": 938,
"cds_end": null,
"cds_length": 1815,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000972135.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000972134.1",
"protein_id": "ENSP00000642193.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 595,
"cds_start": 938,
"cds_end": null,
"cds_length": 1788,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000972134.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000706807.1",
"protein_id": "ENSP00000516564.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 571,
"cds_start": 938,
"cds_end": null,
"cds_length": 1716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706807.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu",
"transcript": "ENST00000706806.1",
"protein_id": "ENSP00000516563.1",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 566,
"cds_start": 938,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706806.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.839C>T",
"hgvs_p": "p.Ser280Leu",
"transcript": "ENST00000706818.1",
"protein_id": "ENSP00000516571.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 554,
"cds_start": 839,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706818.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.755C>T",
"hgvs_p": "p.Ser252Leu",
"transcript": "NM_001319072.2",
"protein_id": "NP_001306001.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 526,
"cds_start": 755,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319072.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.755C>T",
"hgvs_p": "p.Ser252Leu",
"transcript": "NM_001437893.1",
"protein_id": "NP_001424822.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 526,
"cds_start": 755,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437893.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.755C>T",
"hgvs_p": "p.Ser252Leu",
"transcript": "ENST00000438671.4",
"protein_id": "ENSP00000411966.2",
"transcript_support_level": 4,
"aa_start": 252,
"aa_end": null,
"aa_length": 526,
"cds_start": 755,
"cds_end": null,
"cds_length": 1581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000438671.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.629C>T",
"hgvs_p": "p.Ser210Leu",
"transcript": "NM_001319073.2",
"protein_id": "NP_001306002.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 484,
"cds_start": 629,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319073.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.629C>T",
"hgvs_p": "p.Ser210Leu",
"transcript": "ENST00000418611.5",
"protein_id": "ENSP00000396387.1",
"transcript_support_level": 2,
"aa_start": 210,
"aa_end": null,
"aa_length": 484,
"cds_start": 629,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418611.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.629C>T",
"hgvs_p": "p.Ser210Leu",
"transcript": "ENST00000478586.4",
"protein_id": "ENSP00000516562.1",
"transcript_support_level": 4,
"aa_start": 210,
"aa_end": null,
"aa_length": 484,
"cds_start": 629,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000478586.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.86C>T",
"hgvs_p": "p.Ser29Leu",
"transcript": "ENST00000706817.1",
"protein_id": "ENSP00000516570.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 303,
"cds_start": 86,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706817.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "c.-174-6266C>T",
"hgvs_p": null,
"transcript": "ENST00000706803.1",
"protein_id": "ENSP00000516560.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 116,
"cds_start": null,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706803.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "n.85C>T",
"hgvs_p": null,
"transcript": "ENST00000433336.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000433336.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "n.*594C>T",
"hgvs_p": null,
"transcript": "ENST00000441228.5",
"protein_id": "ENSP00000406263.1",
"transcript_support_level": 2,
"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": "ENST00000441228.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "n.*418C>T",
"hgvs_p": null,
"transcript": "ENST00000445499.3",
"protein_id": "ENSP00000516561.1",
"transcript_support_level": 4,
"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": "ENST00000445499.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"hgvs_c": "n.1878C>T",
"hgvs_p": null,
"transcript": "ENST00000463659.2",
"protein_id": null,
"transcript_support_level": 3,
"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,
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"gene_symbol": "SACM1L",
"gene_hgnc_id": 17059,
"dbsnp": "rs1489201353",
"frequency_reference_population": 0.0000068224754,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000616345,
"gnomad_genomes_af": 0.0000131496,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6758314371109009,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.299,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.17,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.542,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001319071.2",
"gene_symbol": "SACM1L",
"hgnc_id": 17059,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.938C>T",
"hgvs_p": "p.Ser313Leu"
}
],
"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
}