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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: 6-43670917-GAGA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=43670917&ref=GAGA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 43670917,
"ref": "GAGA",
"alt": "G",
"effect": "conservative_inframe_deletion",
"transcript": "NM_001424119.1",
"consequences": [
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.804_806delGAA",
"hgvs_p": "p.Lys268del",
"transcript": "NM_152732.5",
"protein_id": "NP_689945.2",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 276,
"cds_start": 804,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372163.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152732.5"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.804_806delGAA",
"hgvs_p": "p.Lys268del",
"transcript": "ENST00000372163.5",
"protein_id": "ENSP00000361236.4",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 276,
"cds_start": 804,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152732.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372163.5"
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.901_903delGAA",
"hgvs_p": "p.Glu301del",
"transcript": "NM_001424119.1",
"protein_id": "NP_001411048.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 321,
"cds_start": 901,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424119.1"
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.856_858delGAA",
"hgvs_p": "p.Glu286del",
"transcript": "NM_001193341.2",
"protein_id": "NP_001180270.1",
"transcript_support_level": null,
"aa_start": 286,
"aa_end": null,
"aa_length": 306,
"cds_start": 856,
"cds_end": null,
"cds_length": 921,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193341.2"
},
{
"aa_ref": "E",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.856_858delGAA",
"hgvs_p": "p.Glu286del",
"transcript": "ENST00000372165.8",
"protein_id": "ENSP00000361238.4",
"transcript_support_level": 2,
"aa_start": 286,
"aa_end": null,
"aa_length": 306,
"cds_start": 856,
"cds_end": null,
"cds_length": 921,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372165.8"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.804_806delGAA",
"hgvs_p": "p.Lys268del",
"transcript": "ENST00000890744.1",
"protein_id": "ENSP00000560803.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 276,
"cds_start": 804,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890744.1"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.759_761delGAA",
"hgvs_p": "p.Lys253del",
"transcript": "NM_001424120.1",
"protein_id": "NP_001411049.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 261,
"cds_start": 759,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001424120.1"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.759_761delGAA",
"hgvs_p": "p.Lys253del",
"transcript": "ENST00000890745.1",
"protein_id": "ENSP00000560804.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 261,
"cds_start": 759,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890745.1"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.720_722delGAA",
"hgvs_p": "p.Lys240del",
"transcript": "ENST00000890746.1",
"protein_id": "ENSP00000560805.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 248,
"cds_start": 720,
"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": "ENST00000890746.1"
},
{
"aa_ref": "KN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "c.459_461delGAA",
"hgvs_p": "p.Lys153del",
"transcript": "ENST00000928837.1",
"protein_id": "ENSP00000598896.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 161,
"cds_start": 459,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928837.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "n.701_703delGAA",
"hgvs_p": null,
"transcript": "NR_187613.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_187613.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"hgvs_c": "n.818_820delGAA",
"hgvs_p": null,
"transcript": "NR_187614.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_187614.1"
}
],
"gene_symbol": "RSPH9",
"gene_hgnc_id": 21057,
"dbsnp": "rs397515340",
"frequency_reference_population": 0.00009788203,
"hom_count_reference_population": 1,
"allele_count_reference_population": 158,
"gnomad_exomes_af": 0.000103293,
"gnomad_genomes_af": 0.0000459553,
"gnomad_exomes_ac": 151,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"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": 6.659,
"phylop100way_prediction": "Uncertain_significance",
"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": "Likely_pathogenic",
"acmg_criteria": "PM4_Supporting,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM4_Supporting",
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001424119.1",
"gene_symbol": "RSPH9",
"hgnc_id": 21057,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.901_903delGAA",
"hgvs_p": "p.Glu301del"
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 12,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7",
"phenotype_combined": "Primary ciliary dyskinesia 12|Primary ciliary dyskinesia|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}