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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: 4-52029852-AAC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=52029852&ref=AAC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 52029852,
"ref": "AAC",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "NM_000232.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.253_254delGT",
"hgvs_p": "p.Val85fs",
"transcript": "NM_000232.5",
"protein_id": "NP_000223.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 318,
"cds_start": 253,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000381431.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000232.5"
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.253_254delGT",
"hgvs_p": "p.Val85fs",
"transcript": "ENST00000381431.10",
"protein_id": "ENSP00000370839.6",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 318,
"cds_start": 253,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000232.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381431.10"
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.253_254delGT",
"hgvs_p": "p.Val85fs",
"transcript": "ENST00000899666.1",
"protein_id": "ENSP00000569725.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 314,
"cds_start": 253,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899666.1"
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.253_254delGT",
"hgvs_p": "p.Val85fs",
"transcript": "ENST00000912466.1",
"protein_id": "ENSP00000582525.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 274,
"cds_start": 253,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912466.1"
},
{
"aa_ref": "V",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.43_44delGT",
"hgvs_p": "p.Val15fs",
"transcript": "NM_001440519.1",
"protein_id": "NP_001427448.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 248,
"cds_start": 43,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440519.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.-45_-44delGT",
"hgvs_p": null,
"transcript": "NM_001440520.1",
"protein_id": "NP_001427449.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": null,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440520.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "c.-45_-44delGT",
"hgvs_p": null,
"transcript": "XM_047416076.1",
"protein_id": "XP_047272032.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": null,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416076.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "n.*35_*36delGT",
"hgvs_p": null,
"transcript": "ENST00000506357.5",
"protein_id": "ENSP00000421235.1",
"transcript_support_level": 5,
"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": "ENST00000506357.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "n.*48_*49delGT",
"hgvs_p": null,
"transcript": "ENST00000514133.1",
"protein_id": "ENSP00000425818.1",
"transcript_support_level": 5,
"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": "ENST00000514133.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "n.*35_*36delGT",
"hgvs_p": null,
"transcript": "ENST00000506357.5",
"protein_id": "ENSP00000421235.1",
"transcript_support_level": 5,
"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": "ENST00000506357.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"hgvs_c": "n.*48_*49delGT",
"hgvs_p": null,
"transcript": "ENST00000514133.1",
"protein_id": "ENSP00000425818.1",
"transcript_support_level": 5,
"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": "ENST00000514133.1"
}
],
"gene_symbol": "SGCB",
"gene_hgnc_id": 10806,
"dbsnp": "rs1553940274",
"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": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.074,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000232.5",
"gene_symbol": "SGCB",
"hgnc_id": 10806,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.253_254delGT",
"hgvs_p": "p.Val85fs"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2E",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2E",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}