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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: 19-40458170-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40458170&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BLVRB",
"hgnc_id": 1063,
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_000713.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.7483,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.06,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7562146782875061,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 206,
"aa_ref": "V",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 799,
"cdna_start": 376,
"cds_end": null,
"cds_length": 621,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_000713.3",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263368.9",
"protein_coding": true,
"protein_id": "NP_000704.1",
"strand": false,
"transcript": "NM_000713.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 206,
"aa_ref": "V",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 799,
"cdna_start": 376,
"cds_end": null,
"cds_length": 621,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000263368.9",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000713.3",
"protein_coding": true,
"protein_id": "ENSP00000263368.3",
"strand": false,
"transcript": "ENST00000263368.9",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 205,
"aa_ref": "V",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 856,
"cdna_start": 457,
"cds_end": null,
"cds_length": 618,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000926837.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596896.1",
"strand": false,
"transcript": "ENST00000926837.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 202,
"aa_ref": "V",
"aa_start": 103,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 810,
"cdna_start": 405,
"cds_end": null,
"cds_length": 609,
"cds_start": 307,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000858750.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.307G>A",
"hgvs_p": "p.Val103Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528809.1",
"strand": false,
"transcript": "ENST00000858750.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 196,
"aa_ref": "V",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 775,
"cdna_start": 411,
"cds_end": null,
"cds_length": 591,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000858752.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528811.1",
"strand": false,
"transcript": "ENST00000858752.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 163,
"aa_ref": "V",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 649,
"cdna_start": 376,
"cds_end": null,
"cds_length": 492,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000595483.5",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.319G>A",
"hgvs_p": "p.Val107Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000471720.1",
"strand": false,
"transcript": "ENST00000595483.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 245,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 938,
"cdna_start": null,
"cds_end": null,
"cds_length": 738,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000643519.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.451+4G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494515.1",
"strand": false,
"transcript": "ENST00000643519.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 196,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 792,
"cdna_start": null,
"cds_end": null,
"cds_length": 591,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000858751.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.304+15G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528810.1",
"strand": false,
"transcript": "ENST00000858751.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 176,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": 531,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000858749.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.244+211G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528808.1",
"strand": false,
"transcript": "ENST00000858749.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 137,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 564,
"cdna_start": null,
"cds_end": null,
"cds_length": 414,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000926838.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "c.171+284G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596897.1",
"strand": false,
"transcript": "ENST00000926838.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1392,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000597870.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "n.319G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000470619.1",
"strand": false,
"transcript": "ENST00000597870.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 676,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000601346.5",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "n.288G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000601346.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 767,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000643596.1",
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"hgvs_c": "n.315+4G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496337.1",
"strand": false,
"transcript": "ENST00000643596.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1050862630",
"effect": "missense_variant",
"frequency_reference_population": 0.000019827721,
"gene_hgnc_id": 1063,
"gene_symbol": "BLVRB",
"gnomad_exomes_ac": 29,
"gnomad_exomes_af": 0.0000198398,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197119,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.984,
"pos": 40458170,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.347,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.1599999964237213,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.16,
"transcript": "NM_000713.3"
}
]
}