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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: 6-98874318-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=98874318&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 98874318,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000369244.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "NM_001278716.2",
"protein_id": "NP_001265645.1",
"transcript_support_level": null,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2275,
"cdna_end": null,
"cdna_length": 8058,
"mane_select": "ENST00000369244.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "ENST00000369244.7",
"protein_id": "ENSP00000358247.1",
"transcript_support_level": 1,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2275,
"cdna_end": null,
"cdna_length": 8058,
"mane_select": "NM_001278716.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "ENST00000229971.2",
"protein_id": "ENSP00000229971.1",
"transcript_support_level": 1,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2217,
"cdna_end": null,
"cdna_length": 2810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "NM_012160.5",
"protein_id": "NP_036292.2",
"transcript_support_level": null,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2157,
"cdna_end": null,
"cdna_length": 7940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "XM_017010726.2",
"protein_id": "XP_016866215.1",
"transcript_support_level": null,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 2157,
"cdna_end": null,
"cdna_length": 7940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"transcript": "XM_047418625.1",
"protein_id": "XP_047274581.1",
"transcript_support_level": null,
"aa_start": 609,
"aa_end": null,
"aa_length": 621,
"cds_start": 1826,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 14857,
"cdna_end": null,
"cdna_length": 20640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1754G>A",
"hgvs_p": "p.Ser585Asn",
"transcript": "XM_005266930.4",
"protein_id": "XP_005266987.1",
"transcript_support_level": null,
"aa_start": 585,
"aa_end": null,
"aa_length": 597,
"cds_start": 1754,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 2203,
"cdna_end": null,
"cdna_length": 7986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1754G>A",
"hgvs_p": "p.Ser585Asn",
"transcript": "XM_017010727.3",
"protein_id": "XP_016866216.1",
"transcript_support_level": null,
"aa_start": 585,
"aa_end": null,
"aa_length": 597,
"cds_start": 1754,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 2085,
"cdna_end": null,
"cdna_length": 7868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1754G>A",
"hgvs_p": "p.Ser585Asn",
"transcript": "XM_047418626.1",
"protein_id": "XP_047274582.1",
"transcript_support_level": null,
"aa_start": 585,
"aa_end": null,
"aa_length": 597,
"cds_start": 1754,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 2085,
"cdna_end": null,
"cdna_length": 7868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "c.1100G>A",
"hgvs_p": "p.Ser367Asn",
"transcript": "XM_047418628.1",
"protein_id": "XP_047274584.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 379,
"cds_start": 1100,
"cds_end": null,
"cds_length": 1140,
"cdna_start": 1390,
"cdna_end": null,
"cdna_length": 7173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"hgvs_c": "n.1811G>A",
"hgvs_p": null,
"transcript": "NR_103836.2",
"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": 7594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FBXL4",
"gene_hgnc_id": 13601,
"dbsnp": "rs371875653",
"frequency_reference_population": 0.000018664214,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000171792,
"gnomad_genomes_af": 0.0000328709,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07241758704185486,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0662,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.144,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 2,
"pathogenic_score": 5,
"criteria": [
"PM1",
"PM2",
"PP2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000369244.7",
"gene_symbol": "FBXL4",
"hgnc_id": 13601,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn"
}
],
"clinvar_disease": "Mitochondrial DNA depletion syndrome 13,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Mitochondrial DNA depletion syndrome 13|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}