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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: 19-54040965-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54040965&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 54040965,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_198481.4",
"consequences": [
{
"aa_ref": "V",
"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.707T>A",
"hgvs_p": "p.Val236Glu",
"transcript": "NM_198481.4",
"protein_id": "NP_940883.2",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 236,
"cds_start": 707,
"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": "V",
"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.707T>A",
"hgvs_p": "p.Val236Glu",
"transcript": "ENST00000338372.7",
"protein_id": "ENSP00000343366.2",
"transcript_support_level": 1,
"aa_start": 236,
"aa_end": null,
"aa_length": 236,
"cds_start": 707,
"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": "V",
"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.614T>A",
"hgvs_p": "p.Val205Glu",
"transcript": "ENST00000376626.5",
"protein_id": "ENSP00000365813.1",
"transcript_support_level": 1,
"aa_start": 205,
"aa_end": null,
"aa_length": 205,
"cds_start": 614,
"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": "V",
"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.347T>A",
"hgvs_p": "p.Val116Glu",
"transcript": "ENST00000366170.6",
"protein_id": "ENSP00000444153.2",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 116,
"cds_start": 347,
"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.*204T>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.*204T>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": "V",
"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.614T>A",
"hgvs_p": "p.Val205Glu",
"transcript": "NM_001288792.2",
"protein_id": "NP_001275721.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 205,
"cds_start": 614,
"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": "V",
"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.443T>A",
"hgvs_p": "p.Val148Glu",
"transcript": "NM_001288791.2",
"protein_id": "NP_001275720.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 148,
"cds_start": 443,
"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": "V",
"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.377T>A",
"hgvs_p": "p.Val126Glu",
"transcript": "ENST00000419106.5",
"protein_id": "ENSP00000409412.1",
"transcript_support_level": 2,
"aa_start": 126,
"aa_end": null,
"aa_length": 126,
"cds_start": 377,
"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": "V",
"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.347T>A",
"hgvs_p": "p.Val116Glu",
"transcript": "NM_001288793.2",
"protein_id": "NP_001275722.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 116,
"cds_start": 347,
"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": "V",
"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.1091T>A",
"hgvs_p": "p.Val364Glu",
"transcript": "XM_011526845.2",
"protein_id": "XP_011525147.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 364,
"cds_start": 1091,
"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": "V",
"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.1001T>A",
"hgvs_p": "p.Val334Glu",
"transcript": "XM_011526846.2",
"protein_id": "XP_011525148.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 334,
"cds_start": 1001,
"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": "V",
"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.908T>A",
"hgvs_p": "p.Val303Glu",
"transcript": "XM_011526848.2",
"protein_id": "XP_011525150.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 303,
"cds_start": 908,
"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": "V",
"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.797T>A",
"hgvs_p": "p.Val266Glu",
"transcript": "XM_011526849.2",
"protein_id": "XP_011525151.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 266,
"cds_start": 797,
"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.*94T>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.916T>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": "rs746783531",
"frequency_reference_population": 0.000013670999,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000116664,
"gnomad_genomes_af": 0.0000328805,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01475343108177185,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.14,
"revel_prediction": "Benign",
"alphamissense_score": 0.215,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.45,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_198481.4",
"gene_symbol": "VSTM1",
"hgnc_id": 29455,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.707T>A",
"hgvs_p": "p.Val236Glu"
}
],
"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
}