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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: 13-23324513-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=23324513&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 23324513,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000218867.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.848G>A",
"hgvs_p": "p.Cys283Tyr",
"transcript": "NM_000231.3",
"protein_id": "NP_000222.2",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 291,
"cds_start": 848,
"cds_end": null,
"cds_length": 876,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 1594,
"mane_select": "ENST00000218867.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.848G>A",
"hgvs_p": "p.Cys283Tyr",
"transcript": "ENST00000218867.4",
"protein_id": "ENSP00000218867.3",
"transcript_support_level": 1,
"aa_start": 283,
"aa_end": null,
"aa_length": 291,
"cds_start": 848,
"cds_end": null,
"cds_length": 876,
"cdna_start": 945,
"cdna_end": null,
"cdna_length": 1594,
"mane_select": "NM_000231.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.902G>A",
"hgvs_p": "p.Cys301Tyr",
"transcript": "NM_001378244.1",
"protein_id": "NP_001365173.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 309,
"cds_start": 902,
"cds_end": null,
"cds_length": 930,
"cdna_start": 987,
"cdna_end": null,
"cdna_length": 1636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.848G>A",
"hgvs_p": "p.Cys283Tyr",
"transcript": "NM_001378245.1",
"protein_id": "NP_001365174.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 291,
"cds_start": 848,
"cds_end": null,
"cds_length": 876,
"cdna_start": 1047,
"cdna_end": null,
"cdna_length": 1696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.848G>A",
"hgvs_p": "p.Cys283Tyr",
"transcript": "NM_001378246.1",
"protein_id": "NP_001365175.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 291,
"cds_start": 848,
"cds_end": null,
"cds_length": 876,
"cdna_start": 1096,
"cdna_end": null,
"cdna_length": 1745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.707G>A",
"hgvs_p": "p.Cys236Tyr",
"transcript": "XM_047430542.1",
"protein_id": "XP_047286498.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 244,
"cds_start": 707,
"cds_end": null,
"cds_length": 735,
"cdna_start": 792,
"cdna_end": null,
"cdna_length": 1441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SACS",
"gene_hgnc_id": 10519,
"hgvs_c": "c.2186-12398C>T",
"hgvs_p": null,
"transcript": "ENST00000682775.1",
"protein_id": "ENSP00000508399.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 739,
"cds_start": -4,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SACS",
"gene_hgnc_id": 10519,
"hgvs_c": "c.2185+29272C>T",
"hgvs_p": null,
"transcript": "ENST00000683210.1",
"protein_id": "ENSP00000506739.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 738,
"cds_start": -4,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SACS",
"gene_hgnc_id": 10519,
"hgvs_c": "c.2186-1869C>T",
"hgvs_p": null,
"transcript": "ENST00000684497.1",
"protein_id": "ENSP00000507057.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 738,
"cds_start": -4,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SACS",
"gene_hgnc_id": 10519,
"hgvs_c": "n.2186-2839C>T",
"hgvs_p": null,
"transcript": "ENST00000684325.1",
"protein_id": "ENSP00000508121.1",
"transcript_support_level": null,
"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": 4333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC107984585",
"gene_hgnc_id": null,
"hgvs_c": "n.-140C>T",
"hgvs_p": null,
"transcript": "XR_001749787.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"dbsnp": "rs104894422",
"frequency_reference_population": 0.0000061618853,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000616189,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9948995113372803,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.962,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8196,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.074,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000218867.4",
"gene_symbol": "SGCG",
"hgnc_id": 10809,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.848G>A",
"hgvs_p": "p.Cys283Tyr"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000682775.1",
"gene_symbol": "SACS",
"hgnc_id": 10519,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2186-12398C>T",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_001749787.2",
"gene_symbol": "LOC107984585",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-140C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2C,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2C|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}