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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: X-53380685-T-TGGCC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53380685&ref=T&alt=TGGCC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53380685,
"ref": "T",
"alt": "TGGCC",
"effect": "frameshift_variant",
"transcript": "NM_006306.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3549_3552dupGGCC",
"hgvs_p": "p.Ile1185fs",
"transcript": "NM_006306.4",
"protein_id": "NP_006297.2",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3552,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 3606,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "ENST00000322213.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006306.4"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3549_3552dupGGCC",
"hgvs_p": "p.Ile1185fs",
"transcript": "ENST00000322213.9",
"protein_id": "ENSP00000323421.3",
"transcript_support_level": 1,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3552,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 3606,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "NM_006306.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322213.9"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3483_3486dupGGCC",
"hgvs_p": "p.Ile1163fs",
"transcript": "ENST00000375340.10",
"protein_id": "ENSP00000364489.7",
"transcript_support_level": 1,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3486,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3826,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375340.10"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3483_3486dupGGCC",
"hgvs_p": "p.Ile1163fs",
"transcript": "NM_001281463.1",
"protein_id": "NP_001268392.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3486,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3826,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281463.1"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3483_3486dupGGCC",
"hgvs_p": "p.Ile1163fs",
"transcript": "ENST00000675504.1",
"protein_id": "ENSP00000502524.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3486,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3722,
"cdna_end": null,
"cdna_length": 9826,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675504.1"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3183_3186dupGGCC",
"hgvs_p": "p.Ile1063fs",
"transcript": "ENST00000947776.1",
"protein_id": "ENSP00000617835.1",
"transcript_support_level": null,
"aa_start": 1062,
"aa_end": null,
"aa_length": 1111,
"cds_start": 3186,
"cds_end": null,
"cds_length": 3336,
"cdna_start": 3263,
"cdna_end": null,
"cdna_length": 5540,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947776.1"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2847_2850dupGGCC",
"hgvs_p": "p.Ile951fs",
"transcript": "ENST00000947777.1",
"protein_id": "ENSP00000617836.1",
"transcript_support_level": null,
"aa_start": 950,
"aa_end": null,
"aa_length": 999,
"cds_start": 2850,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 2937,
"cdna_end": null,
"cdna_length": 4734,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947777.1"
},
{
"aa_ref": "A",
"aa_alt": "AG?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2781_2784dupGGCC",
"hgvs_p": "p.Ile929fs",
"transcript": "ENST00000674590.1",
"protein_id": "ENSP00000502626.1",
"transcript_support_level": null,
"aa_start": 928,
"aa_end": null,
"aa_length": 977,
"cds_start": 2784,
"cds_end": null,
"cds_length": 2934,
"cdna_start": 3124,
"cdna_end": null,
"cdna_length": 3323,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674590.1"
},
{
"aa_ref": "P",
"aa_alt": "PA?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.767_770dupGGCC",
"hgvs_p": "p.Ser258fs",
"transcript": "ENST00000470241.2",
"protein_id": "ENSP00000476416.1",
"transcript_support_level": 3,
"aa_start": 257,
"aa_end": null,
"aa_length": 277,
"cds_start": 770,
"cds_end": null,
"cds_length": 836,
"cdna_start": 772,
"cdna_end": null,
"cdna_length": 838,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470241.2"
}
],
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"dbsnp": "rs863225459",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.436,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_006306.4",
"gene_symbol": "SMC1A",
"hgnc_id": 11111,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.3549_3552dupGGCC",
"hgvs_p": "p.Ile1185fs"
}
],
"clinvar_disease": " 85, with or without midline brain defects,Congenital muscular hypertrophy-cerebral syndrome,Developmental and epileptic encephalopathy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Congenital muscular hypertrophy-cerebral syndrome|Developmental and epileptic encephalopathy, 85, with or without midline brain defects",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}