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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: 5-70938888-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=70938888&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 70938888,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000380707.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "NM_000344.4",
"protein_id": "NP_000335.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 294,
"cds_start": 131,
"cds_end": null,
"cds_length": 885,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1482,
"mane_select": "ENST00000380707.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000380707.9",
"protein_id": "ENSP00000370083.4",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 294,
"cds_start": 131,
"cds_end": null,
"cds_length": 885,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1482,
"mane_select": "NM_000344.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000351205.8",
"protein_id": "ENSP00000305857.5",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 294,
"cds_start": 131,
"cds_end": null,
"cds_length": 885,
"cdna_start": 131,
"cdna_end": null,
"cdna_length": 900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000506163.5",
"protein_id": "ENSP00000424926.1",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 282,
"cds_start": 131,
"cds_end": null,
"cds_length": 849,
"cdna_start": 140,
"cdna_end": null,
"cdna_length": 1445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000625245.2",
"protein_id": "ENSP00000486539.1",
"transcript_support_level": 5,
"aa_start": 44,
"aa_end": null,
"aa_length": 294,
"cds_start": 131,
"cds_end": null,
"cds_length": 885,
"cdna_start": 131,
"cdna_end": null,
"cdna_length": 885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "NM_001297715.1",
"protein_id": "NP_001284644.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 282,
"cds_start": 131,
"cds_end": null,
"cds_length": 849,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "NM_022874.2",
"protein_id": "NP_075012.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 262,
"cds_start": 131,
"cds_end": null,
"cds_length": 789,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000503079.6",
"protein_id": "ENSP00000428128.1",
"transcript_support_level": 5,
"aa_start": 44,
"aa_end": null,
"aa_length": 262,
"cds_start": 131,
"cds_end": null,
"cds_length": 789,
"cdna_start": 205,
"cdna_end": null,
"cdna_length": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "ENST00000514951.5",
"protein_id": "ENSP00000423298.1",
"transcript_support_level": 2,
"aa_start": 44,
"aa_end": null,
"aa_length": 227,
"cds_start": 131,
"cds_end": null,
"cds_length": 684,
"cdna_start": 179,
"cdna_end": null,
"cdna_length": 1308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_047417615.1",
"protein_id": "XP_047273571.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 295,
"cds_start": 131,
"cds_end": null,
"cds_length": 888,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_011543596.2",
"protein_id": "XP_011541898.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 294,
"cds_start": 131,
"cds_end": null,
"cds_length": 885,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_047417616.1",
"protein_id": "XP_047273572.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 262,
"cds_start": 131,
"cds_end": null,
"cds_length": 789,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_017009786.2",
"protein_id": "XP_016865275.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 250,
"cds_start": 131,
"cds_end": null,
"cds_length": 753,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_011543597.2",
"protein_id": "XP_011541899.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 227,
"cds_start": 131,
"cds_end": null,
"cds_length": 684,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val",
"transcript": "XM_047417618.1",
"protein_id": "XP_047273574.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 215,
"cds_start": 131,
"cds_end": null,
"cds_length": 648,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 1373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"hgvs_c": "n.131A>T",
"hgvs_p": null,
"transcript": "ENST00000506239.6",
"protein_id": "ENSP00000422679.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMN1",
"gene_hgnc_id": 11117,
"dbsnp": "rs104893931",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9722830057144165,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.95,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9947,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.351,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000380707.9",
"gene_symbol": "SMN1",
"hgnc_id": 11117,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.131A>T",
"hgvs_p": "p.Asp44Val"
}
],
"clinvar_disease": "Kugelberg-Welander disease",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Kugelberg-Welander disease",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}