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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: 19-54040977-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54040977&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 54040977,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_198481.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.695C>A",
"hgvs_p": "p.Ala232Glu",
"transcript": "NM_198481.4",
"protein_id": "NP_940883.2",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 236,
"cds_start": 695,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000338372.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198481.4"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.695C>A",
"hgvs_p": "p.Ala232Glu",
"transcript": "ENST00000338372.7",
"protein_id": "ENSP00000343366.2",
"transcript_support_level": 1,
"aa_start": 232,
"aa_end": null,
"aa_length": 236,
"cds_start": 695,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198481.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338372.7"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.602C>A",
"hgvs_p": "p.Ala201Glu",
"transcript": "ENST00000376626.5",
"protein_id": "ENSP00000365813.1",
"transcript_support_level": 1,
"aa_start": 201,
"aa_end": null,
"aa_length": 205,
"cds_start": 602,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376626.5"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.335C>A",
"hgvs_p": "p.Ala112Glu",
"transcript": "ENST00000366170.6",
"protein_id": "ENSP00000444153.2",
"transcript_support_level": 1,
"aa_start": 112,
"aa_end": null,
"aa_length": 116,
"cds_start": 335,
"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": "ENST00000366170.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "n.*192C>A",
"hgvs_p": null,
"transcript": "ENST00000447872.5",
"protein_id": "ENSP00000401926.1",
"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": "ENST00000447872.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "n.*192C>A",
"hgvs_p": null,
"transcript": "ENST00000447872.5",
"protein_id": "ENSP00000401926.1",
"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": "ENST00000447872.5"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.602C>A",
"hgvs_p": "p.Ala201Glu",
"transcript": "NM_001288792.2",
"protein_id": "NP_001275721.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 205,
"cds_start": 602,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001288792.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.431C>A",
"hgvs_p": "p.Ala144Glu",
"transcript": "NM_001288791.2",
"protein_id": "NP_001275720.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 148,
"cds_start": 431,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001288791.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.365C>A",
"hgvs_p": "p.Ala122Glu",
"transcript": "ENST00000419106.5",
"protein_id": "ENSP00000409412.1",
"transcript_support_level": 2,
"aa_start": 122,
"aa_end": null,
"aa_length": 126,
"cds_start": 365,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419106.5"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.335C>A",
"hgvs_p": "p.Ala112Glu",
"transcript": "NM_001288793.2",
"protein_id": "NP_001275722.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 116,
"cds_start": 335,
"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": "NM_001288793.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.1079C>A",
"hgvs_p": "p.Ala360Glu",
"transcript": "XM_011526845.2",
"protein_id": "XP_011525147.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 364,
"cds_start": 1079,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526845.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.989C>A",
"hgvs_p": "p.Ala330Glu",
"transcript": "XM_011526846.2",
"protein_id": "XP_011525148.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 334,
"cds_start": 989,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526846.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.896C>A",
"hgvs_p": "p.Ala299Glu",
"transcript": "XM_011526848.2",
"protein_id": "XP_011525150.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 303,
"cds_start": 896,
"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": "XM_011526848.2"
},
{
"aa_ref": "A",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.785C>A",
"hgvs_p": "p.Ala262Glu",
"transcript": "XM_011526849.2",
"protein_id": "XP_011525151.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 266,
"cds_start": 785,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526849.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "c.*82C>A",
"hgvs_p": null,
"transcript": "XM_011526847.2",
"protein_id": "XP_011525149.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": null,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526847.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"hgvs_c": "n.904C>A",
"hgvs_p": null,
"transcript": "NR_110142.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_110142.2"
}
],
"gene_symbol": "VSTM1",
"gene_hgnc_id": 29455,
"dbsnp": "rs146430350",
"frequency_reference_population": 0.0000049701544,
"hom_count_reference_population": 1,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000480253,
"gnomad_genomes_af": 0.00000657704,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08683496713638306,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.086,
"revel_prediction": "Benign",
"alphamissense_score": 0.1408,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.611,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_198481.4",
"gene_symbol": "VSTM1",
"hgnc_id": 29455,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.695C>A",
"hgvs_p": "p.Ala232Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}