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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: 2-189791888-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189791888&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 189791888,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000534.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "NM_000534.5",
"protein_id": "NP_000525.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000441310.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000534.5"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000441310.7",
"protein_id": "ENSP00000406490.3",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000534.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441310.7"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"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": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000374826.8",
"protein_id": "ENSP00000363959.4",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 165,
"cds_start": 79,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374826.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "n.79G>C",
"hgvs_p": null,
"transcript": "ENST00000424059.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000424059.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921104.1",
"protein_id": "ENSP00000591163.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 968,
"cds_start": 79,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921104.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921113.1",
"protein_id": "ENSP00000591172.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 953,
"cds_start": 79,
"cds_end": null,
"cds_length": 2862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921113.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921105.1",
"protein_id": "ENSP00000591164.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 940,
"cds_start": 79,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921105.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "NM_001321045.2",
"protein_id": "NP_001307974.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321045.2"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "NM_001321047.2",
"protein_id": "NP_001307976.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321047.2"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "NM_001321048.2",
"protein_id": "NP_001307977.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321048.2"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000899827.1",
"protein_id": "ENSP00000569886.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899827.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000899828.1",
"protein_id": "ENSP00000569887.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899828.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000899829.1",
"protein_id": "ENSP00000569888.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899829.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000899832.1",
"protein_id": "ENSP00000569891.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899832.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921101.1",
"protein_id": "ENSP00000591160.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921101.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921103.1",
"protein_id": "ENSP00000591162.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921103.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921115.1",
"protein_id": "ENSP00000591174.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921115.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000961092.1",
"protein_id": "ENSP00000631151.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 932,
"cds_start": 79,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961092.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921111.1",
"protein_id": "ENSP00000591170.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 931,
"cds_start": 79,
"cds_end": null,
"cds_length": 2796,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921111.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000921109.1",
"protein_id": "ENSP00000591168.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 915,
"cds_start": 79,
"cds_end": null,
"cds_length": 2748,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921109.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "ENST00000961091.1",
"protein_id": "ENSP00000631150.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 901,
"cds_start": 79,
"cds_end": null,
"cds_length": 2706,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961091.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln",
"transcript": "NM_001128143.2",
"protein_id": "NP_001121615.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 893,
"cds_start": 79,
"cds_end": null,
"cds_length": 2682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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"feature": "NR_110332.2"
}
],
"gene_symbol": "PMS1",
"gene_hgnc_id": 9121,
"dbsnp": "rs5742973",
"frequency_reference_population": 0.000084885854,
"hom_count_reference_population": 1,
"allele_count_reference_population": 137,
"gnomad_exomes_af": 0.0000711515,
"gnomad_genomes_af": 0.000216732,
"gnomad_exomes_ac": 104,
"gnomad_genomes_ac": 33,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3039824366569519,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.824,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9348,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.957,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BP4,BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000534.5",
"gene_symbol": "PMS1",
"hgnc_id": 9121,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.79G>C",
"hgvs_p": "p.Glu27Gln"
}
],
"clinvar_disease": "Polyp of colon,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Polyp of colon|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}