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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: 7-193451-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=193451&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 193451,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000313766.6",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "c.252C>A",
"hgvs_p": "p.Asn84Lys",
"transcript": "NM_020223.4",
"protein_id": "NP_064608.2",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 584,
"cds_start": 252,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 3176,
"mane_select": "ENST00000313766.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "c.252C>A",
"hgvs_p": "p.Asn84Lys",
"transcript": "ENST00000313766.6",
"protein_id": "ENSP00000322323.5",
"transcript_support_level": 1,
"aa_start": 84,
"aa_end": null,
"aa_length": 584,
"cds_start": 252,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 3176,
"mane_select": "NM_020223.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "c.252C>A",
"hgvs_p": "p.Asn84Lys",
"transcript": "XM_047420625.1",
"protein_id": "XP_047276581.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 383,
"cds_start": 252,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 4964,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "n.881C>A",
"hgvs_p": null,
"transcript": "XR_001744837.2",
"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": 2221,
"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": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "n.881C>A",
"hgvs_p": null,
"transcript": "XR_007060116.1",
"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": 2300,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"hgvs_c": "n.881C>A",
"hgvs_p": null,
"transcript": "XR_007060117.1",
"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": 1723,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000240093",
"gene_hgnc_id": null,
"hgvs_c": "n.233+497G>T",
"hgvs_p": null,
"transcript": "ENST00000467050.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 685,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000240093",
"gene_hgnc_id": null,
"hgvs_c": "n.197+259G>T",
"hgvs_p": null,
"transcript": "ENST00000815924.1",
"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": 2105,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000240093",
"gene_hgnc_id": null,
"hgvs_c": "n.131+1060G>T",
"hgvs_p": null,
"transcript": "ENST00000815925.1",
"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": 582,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000240093",
"gene_hgnc_id": null,
"hgvs_c": "n.131+1060G>T",
"hgvs_p": null,
"transcript": "ENST00000815928.1",
"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": 566,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000240093",
"gene_hgnc_id": null,
"hgvs_c": "n.131+1060G>T",
"hgvs_p": null,
"transcript": "ENST00000815929.1",
"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": 1036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FAM20C",
"gene_hgnc_id": 22140,
"dbsnp": "rs190382829",
"frequency_reference_population": 0.00032626538,
"hom_count_reference_population": 3,
"allele_count_reference_population": 477,
"gnomad_exomes_af": 0.000160236,
"gnomad_genomes_af": 0.00176317,
"gnomad_exomes_ac": 210,
"gnomad_genomes_ac": 267,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005661904811859131,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.292,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1274,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.564,
"phylop100way_prediction": "Benign",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000313766.6",
"gene_symbol": "FAM20C",
"hgnc_id": 22140,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.252C>A",
"hgvs_p": "p.Asn84Lys"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000467050.2",
"gene_symbol": "ENSG00000240093",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.233+497G>T",
"hgvs_p": null
}
],
"clinvar_disease": "FAM20C-related disorder,Inborn genetic diseases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "not provided|FAM20C-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}